After you submit your AACOMAS primary application it is out of their hands. So, if you've submitted and listed classes as in progress/future they will not be waiting for those transcripts. They will verify based on the transcripts you send them.
When you start receiving secondaries all the required information will be sent to the schools by you. At this point, AACOMAS is out of the application process. If you want schools to have your updated coursework then you can send them new transcripts but it is not necessary unless, of course, the school requests them.
The schools will know all the courses you listed on the AACOMAS application. Let's say you don't finish summer classes until September and you've sent in your AACOMAS and your transcripts are received by AACOMAS next week. They will verify all your grades except your summer and future grades as there is nothing yet to verify. So, if you took Intro to Fish Breeding over the summer and plan to take Advanced Eel Genetics this fall they will know that. However, they will not know your grades unless you send them directly to the schools. It's possible they'll ask you about these courses during interviews.
Also, you are not obligated to take the courses listed on your primary application unless those courses are prerequisites for the school. You should okay any class changes with your med school just to be sure, though.
When you are accepted you will send final transcripts to the school.