-the corp only draws 1 card every turn unless he uses a click right? also you start with 5 cards but the first step of the turn is draw a card does that mean on turn 1 you start with 6?
Draw 1 card, then you have 3 actions. Yes, start of game is draw 5 for both sides but then corp gets its regular draw, which would be to 6.
-when an agenda has been advanced and you score it what happens to the advancement tokens? they just go back into the bank?
Yes.
-does the ice in front of your central server protect your RD, HQ and archives?
You have three central servers, so the ICE only protects whichever central server its placed on. Your identity card represents your hand/HQ for purposes of putting down ICE.
-after you score an agenda any ice protecting it gets discarded?
No, ICE remains. ICE also remains even after a Runner has passed it.
-when a runner makes a run do they choose a program or is it the combined str of all vs the ice?
In order to break subroutines, you have to first have a breaker that can "interact" with that ICE's subroutines, meaning that it must be the right type of breaker and have strength equal to or greater than the ICE (after any buffing). You can then pay per your icebreaker effects to break as many and whichever subroutines you want. Just remember about ICE, you don't NEED to break subroutines to pass it. If you don't break subroutines, you just get hit with their effects and if "end the run" is not an effect, then you continue if you've survived.