I don’t know about AAMCOMAS, but it takes a fair amount of time to do the AMCAS application. I’m assuming you are applying this year? If so, you should go ahead and register on AMCAS and etc. and start entering info in. You don’t have to pay anything until you actually submit the application. If you have your essay done, most of the AMCAS application is relatively mindless. And, you can skip around and finish the essay later. I would work on my AMCAS on study breaks.
If you don’t have them already, you should get personal copies of all your transcripts (you will need them to enter your courses into the application). One of the first parts of the AMCAS I did was to enter all of my colleges attended, print off the transcript request forms, and get my transcripts submitted to AMCAS. A lot of the complaining people do about how long it takes AMCAS to verify their application has to with, IMO, the fact that they hadn’t requested their transcripts to be sent in until about the same time that they submitted the application. Your application doesn’t even go in line to be verified until AMCAS has all of your transcripts. So, by getting your transcripts taken care of early in your filling out the application, you can speed up the verification process after you actually submit.
You should also be working on getting your letters of recommendation around. Some schools will send you secondary applications as soon as they get your primary application (without MCAT scores). Have your letters ready, so that once you get a secondary, you can immediately have those sent. LOR’s are a primary reason people’s application files don’t become “complete” in a timely manner.
I don’t know that the applications should influence your MCAT study time significantly, unless you already have limited time to devote to it. I found the AMCAS extremely tedious, so I think its a good idea to split it up into smaller sessions over the course of a couple of weeks.