In Reply to: Alcohol arriving through domestic posted by Chris on Tuesday, 1. November 2011 at 16:27 Bali Time:
will be conducted at your first port of call in Indonesia (Probably Jakarta??)
Once you are in Indonesia it's pretty much the same as any domestic flights anywhere.
Most domestic airports will have a small tax to be paid prior to departure.
Duty free should probably be in your checked luggage as I'm not sure about carry on regulations once in transit.