I wouldn't really bother about upgrading your stuff until about lv50. That is when you are going to start to need it, and so it is probably a good idea to start a bit before that to the hang of things. You don't need it early on, at best I would say to buy something from the AH that is already made should you need a little boost. For example I used the Iron Coffin chain set (lv 25) from FA until about level 40.
Anything you do before this really is just for fun. If you do use the AH, shop around as prices can vary wildly, and it is very difficult to weigh up how good value something is. Best is to buy something that is not bound, so when you are done with it you can sell it on, perhaps even for a profit.
1. See above.
2. Tiering - mainly for weapons. Each additional tier gives a 10% bonus to the inherent stats of an item, such as weapon damage, armour defence and what is known as ghost stats, un-named stats that are built into the piece. As I say this is mainly for weapons as this is the only way that you can increase your damage.
You can also use this on armour as it will increase the defence and the stats, but that is very expensive as you need three times the number of manastones to increase the tier by one level. You will end up statting your armour to increase your base stats, this is more important than the defence, as stamina and wisdom also increase your physical and magical defence.
Jewels - plussing your items gives an inherent bonus. Each armour type and slot has its own stat. There is a table kicking about somewhere that gives what each item will give when refined. So chain gloves will give strength, and chain legs dexterity as an example if memory serves right. Your jewellery adds things like crit damage and chance I think, haven't done much work on my baubles. Weapons give physical or magical attack.
Runes - you can stick any rune on any item, and it does what it says on the tin. Each item can only hold 4 runes, and you need to drill the slots with items from the itemshop if they are not already there.
3. Aggregators are purely about your looks. If you really like your Logar robe, when you are lv75 and wearing Sirloth's flayed hide lederhausen with super-duper-kill-everything-by-looking-at-it stats, you can aggregate it with your Logar robe to keep all the stats and properties of your end-game item, but it will look like your Logar robe.
Further to your last question, you can't replace stats. Well you can clean items with an Attribute Cleaning Stone (or whatever it is called) but that is very expensive. Normally though if you have a Logar set with Logar stats and you want better stats, you get a new piece of equipment and start again.
Have a look at this guide for the AT,
https://forum.runesofmagic.com/showthread.php?t=85231
And browse a bit in the guide section, there is some good information in there.
Anything else you want to know just ask.