So, the app that you fill out at aacomas.org is your primary application. Aacomas will process this, check out your classes, GPA, MCAT, etc. and then send it on to the schools which you have designated.
Once the schools receive this primary app, should they find you worthy 👍 , they will email/snail mail/invite you to download their secondary application. Some schools seem to pretty much send everyone a secondary, while others are more selective. Some secondaries are quite simple to fill out (ie.AZCOM - attach resume and a couple questions) and some are quite lengthy (COMP- pages of questions). Most are in between, but you will definitely want to allow yourself time to write some good essays/answers for the secondary questions, showing why DO and why this particular school. (Get started early - Many secondaries are available for download and the questions are floating are floating around SDN - try a search)
Then you send the secondary back, along with the small matter of a check for ~50-75 $'s, and then you wait. and wait. and wait. and hopefully get an interview. That's the nutshell version - I'm sure a lot of folks around here can add more.