If I recall, on AACPMAS, you're filling out the REQUIRED courses only (read the [Instructions] on top), and there's a section where you put in your cum GPA and sci GPA when they ask you for the colleges you have attended.
The other courses (unless they fit into the "required" course category)...ie. religion, will show up on your transcript for them to see, and you don't input that into the application online... someone double check and confirm that with me. 😎 I believe the only contribution the other courses would have in the AACPMAS online application is calculated in the GPA.
I had the same questions, and I recall just inputting all the major sciences/English courses in. I had to pick and choose a few to go in because not everything could be categorized under the appropriate headings (I had a course that fit under all the Bio, Chem, Physics topics). The admissions committee will look everything over again and ask you for details if they have questions.
Good luck. 👍