1) Does BCIS mark any thing on my AP when I am leaving?
Nope, nothing when leaving. You just have to submit your I-94 card to the airline.
2) When I am back with AP, does BCIS keep both originals of AP?
Nope, they just stamp on it and give it back to you. Also, you just need 1 of them.
3) Any other advaces/suggestions?
AP people stand in a different queue than H1Bs. You too need the white I-94 form filled out. Take your I-485 and EAD ... just in case.
Have a safe trip!