submit your primary app to AMCAS before you get your 2nd score because it takes AMCAS like a month to verify your grades and whatnot. only add the minimum of ONE school on the AMCAS application when you first submit your primary. if you are confident that you will get a certain MCAT score, I suppose you can submit your primary to other schools so that they start sending out your secondaries. i DEFINITELY would not submit secondaries until you know your 2nd MCAT score. you could risk wasting a lot of money if you get a low score and submitted your secondaries assuming you would have a higher one.
most schools who pre-secondary screen will wait for your 2nd MCAT as long as you indicated you are retaking it on your primary app, so you don't have to worry about getting screened out pre-2nd MCAT score.
if you submit all your primaries before your 2nd MCAT score, you still have the potential of wasting money if you applied to like WashU and your MCAT comes back as a 28 instead of a 38. you'll end up wasting ~$20/school (I think?). if you submit your secondaries too soon and get a bad score, you have the potential of losing $120/school.
also, it only takes AMCAS 1-2 days to submit your primary to schools after you add them to your list. what takes a long time is AMCAS verifying your transcripts. that can take anywhere from 1 week (if they get your grades on June 1st) to 4+ weeks (if you submit later in the summer). there's really no reason to submit your primary to AMCAS with more than one school on your list because you can just add the rest of your schools right after you are verified. the additional schools would receive your primary 1-2 days after that first school. this is assuming that you are watching over your AMCAS app and catch exactly when AMCAS verifies your primary. keep checking the status page to see when it's complete.
