I applied last cycle so my basic ans will be from last year. when you enter your classes on the PTCAS course page you will list ALL classes/ALL schools (tedious) taken and PLANNED - anything that is not on a current transcript. You have to submit that in order for your app to be processed along w/ them receiving your official transcripts. Your file is incomplete if they don't have your transcripts, many have missed out of early decision due to late transcripts, so I don't recommend waiting. You can enter Planned courses for all the summer and this fall, I even entered for the spring of graduation year. Then in Dec when the AU opens you will send a new set of transcripts to PTCAS that will reflect all the summer and completed fall courses. you will then also be able to update the planned classes you have in PTCAS. the transcripts have to be received by sometime in Jan/Feb (check the instructions) PTCAS is pretty good about ans. your questions--per phone. I never bothered w/ emailing questions. They do have a facebook page which is helpful because alot of people ask questions and PTCAS answers. and the schools / dept are helpful as far as advising you as to what courses they need for prereqs. If not taken put them in the planned semester list.
I also found the program manual instructions for PT programs admin.......helpful from that prospective.....
http://www.apta.org/uploadedFiles/A..._Resources/APTA/PTCAS/PTCAS_ProgramManual.pdf
You can try googling to find the new manual.........2012-13
READ ALL THE INSTRUCTIONS carefully and several times and while completing the app. It's easy to miss info. especially about which courses to use for the prereqs.
Good Luck I remember how stressful the application process was and the relief when done. Then the waiting begins. No finger nails left lol.