Each piece must be performed without editing, but you can edit together several pieces. This way you can record the 12 pieces for all the schools you apply to and then edit together each individual take that you like for each school. Hope that makes sense!
As someone else mentioned, just make sure your sound levels are even when you put the prescreen together. Some schools have you submit each piece separately and others have you edit them together. It is a pain, so the earlier you start the better!