I am so confused with the ins Creed story... PLEASE HELP!!?

Ok so i have beat AC2 and ACB twice but i am so confused with everything about subject 16 and those who came before. If you can help me that would be amazing, and in the Da Vinci Disappearance, the guys talkiing at the end were the same people talking at the end of ACB right? but who are they? and how was Desmond in the Animus if he was in the vault...... If you can help explain this please do! thanks !!