Properly managing your skills, weapons, and other equipment is very important to maintaining as strong a version of yourself as possible. This page will cover what you'll need to know for these things, as well as provide a general idea of what you need to do in order to fully complete the game.
Skills
When you first take a look at your skill tree at the start of the game, you'll notice a few things. Each skill requires a certain number of skill points to acquire, with the most you'll need for a skill being three. Next up are the Master Skills, of which there are one of each for each branch in the tree. These can be earned multiple times, and stack with each time you earn them. As for progressing through the tree, there's one thing about these skills that's different from most other games. If you want to earn the Master Warrior skill, for example, you'll only need to earn just one of the skills connected to it as opposed to all of them. Because of this, the earliest you can earn one of these skills is at around Lv10, but you'll want to invest in all of these skills anyway; many of them are very useful, and lots of them are tied to achievements. Optimally, you'll want to unlock all of these skills, including the ones that are added with the DLC.
Skill points can be earned past your level cap, whether that be Lv40 from the base game or higher with DLC, so you don't need to worry about saving up points too much. However, if you do plan on 100%ing the game's DLC, you should buy both as soon as you can. The Curse of the Pharaohs DLC adds an achievement for reaching Lv55, and you wouldn't want any experience to be "wasted" when you could've been progressing to such a high level. The DLC includes additional skills as well.
After reaching Lv55, you'll earn a new skill point every 20,000XP or so that you earn from that point on. That's about half as much as it takes to get to Lv55 from Lv54, so getting to that level should be a pretty high priority if you can help it.
The Warrior
The Warrior branch focuses on combat, as you could have probably guessed. From the perspective of someone who usually tries to sneak around and has finished the game using mostly only their fists when possible, I would consider the Adrenaline 1 and Adrenaline 2 skills to be of most importance. Since you'll likely not want to run around the same way for the entire game, you should take a look at the skills and judge which of the skills are most important to you. The previously mentioned skills are useful for any type of combat style, so you can't go wrong with those.
There are only two achievements that can be considered to The Warrior. The first is for killing three enemies with a single attack. This is a cinch at a high level after returning to Siwa and using a wide swinging weapon when surrounded by enemies. You can alternatively attack three enemies until they lose all their health while you're unarmed; this doesn't technically kill the enemies, so if three are close enough together on the ground you can swing next to them and hope for the best. Downed enemies cannot be picked up unless they're dead, however, so the first method is probably your best bet.
The second achievement is for finishing an arena boss with an Overpower attack. You can find more information on the arena on the Faiyum Oasis page, but the more important part of this is that you should at least make some attempt to upgrade your Overpower skill using other skills found later in the Warrior skill tree.
The Hunter
The Hunter branch is composed mostly of both archery- and assassination-related skills. Investing in this tree early will greatly increase your potential with bows and the various types of arrows, and is the best skill tree for anyone who likes to sneak around as opposed to running through enemies with a giant mace. These skills are also useful for the more combat-oriented as well, so don't hesitate to look into this tree when you have the chance.
For the first achievement, you need to kill ten enemies in a row without entering combat. This is easiest done with sneak attacks and arrows, of course, but if you're going unarmed, you need to shoot an arrow into your fallen enemies to actually count a kill. This shouldn't be too hard if you're paying close attention to the enemies in a populated area.
Acquire the Enhanced Predator Bow skill perk and use it to kill an enemy that's at least 60m away for another achievement. You can check the distance between you and an enemy by marking him with Senu. It might be a good idea to try this on a sleeping enemy since that'd be the easiest way to make sure your target isn't moving. A good place for this might be the Psenemphaia Hideout, which is next to the northernmost viewpoint in Sapi-Res Nome.
For the next achievement, you need the Elite Ranger perk. This one is a bit less complicated since all you have to do for this one is get a headshot while its slow-motion effects are in play. Alexandria is filled with buildings and enemies, making for a great sniping spot against lower-leveled enemies. I personally got this at Alexandria's Akra Garrison, to the southeast of the city's fast travel point.
Alongside the DLC is an achievement for having Senu harass someone once you have the Eagle Harass skill. When someone is being harassed, perform a headshot on them to get the achievement.
The Seer
The Seer branch consists of skills related to tools and other weapons, like bombs, sleep darts, and so on, and also has some "miscellaneous" skills to boot. For those not too interested in something like smokescreens, you can always look at the Salesman, Buy Materials, and Backstore perks, which greatly affect your buying and selling prowess. Another very useful skill is the Breath Holding Champion skill, which increases the amount of time you can stay underwater.
For the first two achievements in this set, you'll want to learn the Sleep Darts and Animal Taming skills and go to Camp Pyrrhos in Sapi-Res Nome. Kill the enemies there and tame a lion after shooting a sleep dart at it, then take it to a crocodile in the waters to the north. Once they start fighting, you should get the second of these achievements.
For the next achievement, you only have to use the Dawn & Dusk skill 30 times total. You'll be doing this fairly often if you have the perk early on in the game, so you probably won't have to boost this out.
For the most complicated Seer achievement, you need to have Poison Darts and preferably the Pyromaniac skill. Find an enemy that's at least Lv35, shoot a poison dart at him, and then kill him with your torch. The higher level you are, the easier it'll be to kill him, so keep that in mind if your level cap is Lv55 with the DLC.
Inventory
When you look at your gear, you'll see 14 different areas that can be customized. You can hold up to two different bows at once from your selection, as well as two melee weapons, but these extra slots must be unlocked with skills. Next up are the outfits and mounts; outfits don't have any bonuses or anything tied to them, but you can get a few little nods back to earlier Assassin's Creed titles by checking the Ubisoft Club. Mounts, however, vary in performance, with camels being slower than horses and horses being slower than chariots. Shields are important for one-handed weapon builds, and tools are items like the fire bomb and sleep dart, which you can unlock through The Seer skill tree. Below all of this are your six equipment slots, which you can read up on below.
Weapons
By clicking on your melee weapons for the first time, you'll notice that you can sort them by their type, their level, and the last weapon you've looked at. Managing them by type (called categories in the in-game menu) is probably your best bet in the early game, since you won't have too many to look at and you'll be able to learn which weapons are used in which ways. Regular Swords work alongside your Shield slot, Dual Swords obviously take up two hands, and so on. Unarmed combat means that you'll be fighting with your bare hands, and won't actually be killing enemies when their health is taken down. Aside from that, Unarmed doesn't do anything special, but it'll be harder to take down enemies.
There are four types of bows in the game. Hunter bows are your standard bow, nothing special. Light bows allow you to fire very quickly in exchange for damage output. The warrior bow is a similar concept, but you'll be able to fire several arrows at once time like a shotgun as opposed to one at a time rapidly like the light bows do. The last type of bow is the predator bow, which has a sight on it and has a far smaller ammo capacity. All of the capabilities of the bows are best improved upon in the Hunter skill tree.
Shields are what you use to block attacks, of course. They're given differing bonuses unlike the melee weapons and bows, so you need to pay more attention to them. If you don't plan on using shields, however, you'll want to focus on equipping the shield with the highest HP stat anyway; this HP is added to your own regardless of whether or not you use it, so upgrading your favorite or finding a better one can be pretty important.
Tools are items such as poison darts, smokescreens, and sleep darts. These are always useful to have unlocked when you're stuck in a weird situation. When you unlock your first tool, you'll be able to upgrade your new piece of equipment, the tool pouch.
All types of weapons and shields have their own required level that must be reached before you can use them. Each weapon and shield has some bonus effect added to it. The same weapon or shield has the same stats as another with the same name; if you have two Rusty Swords, they'll have the same stats and abilities at the same level. Because of this, there's no need to hold onto two of the same item, so you may as well sell them when you get the chance.
Despite the below achievement's description, you should aim to have two legendary bows, two legendary melee weapons, a legendary shield, outfit, and finally a mount. You need two specific perks to hold two melee weapons and bows at once, so those are prerequisites to the achievement. As for a mount, you should be able to buy one more easily with the Chariot Owner perk and the ones leading up to it. Outfits can be bought from tailors, but you can also get tons of legendary outfits from the Ubisoft Club and will earn others by progressing through the game.
Equipment
Your equipment is very important, and you should focus on improving it very early on into the game. Doing so will require more and more crafting materials, but you can at least pin your hunt for these materials in the menu. You can even see how much your stats would improve by hovering over each piece of equipment and looking at the bottom of your screen. Some equipment will naturally be more important for you to upgrade based on your playstyle, but having all of it as best as can be is never a bad thing to strive for.
It takes a LOT of materials to fully upgrade all six pieces of equipment to their base game maximum, which isn't even necessary, but you'll want to upgrade them a cumulative total of 20 times. The later upgrades require carbon crystals (diamonds), which are hard to come by, but there are enough in the base game locations for you to avoid purchasing them. When upgrading, go with whatever you actually use as a first priority; the breastplate is always a great pick since you'll always want more health.
The Hidden Ones DLC adds a few more upgrade levels to your equipment. The Curse of the Pharaohs DLC also adds more upgrade levels, but you can only perform these final upgrades by using Star Shards found in the DLC's special areas. There's an achievement for making at least one of these final enhancements.
Completion
As you travel across Egypt, you'll be given the chance to complete everything the game has to offer. You'll have to do most of it for the achievements below, and to make things a bit easier for you, each region of the country has been given its own page to isolate its quests and locations from another. You can filter out completed locations with 
to more easily find unfinished locations if you're having trouble finding something in an area.
You don't need to finish all of the side quests to earn the end goal achievement, nor do you have to destroy the Ptolemy statues or finish the Papyrus Puzzles, but if you're enjoying the game, you may as well, right? Quests are given more detail in the first region they appear in -- if a quest starts in one region and has you travel elsewhere, then the info for the quest will be on the page for the starting region. And if you were wondering, Ptolemy statues can be broken with just your fists (or even by throwing torches at them), so if you're trying to go for a fists-only playthrough, you're in luck on that front.
The achievements below are listed here because there's no way of gauging which of the locations you'll be finishing last, as each person playing the game will want to tackle things differently. Stone Circles, for example, are in multiple regions, so those will be given detail on the regions they appear in, but the achievement is listed here since you could go about them at any order you feel like. The Serqet locations for the last achievement here are in the DLC areas of The Curse of the Pharaohs.
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