if medical schools use the AMCAS (a few handful dont), then you will not be sending your transcripts to the individual schools - Once you sign up for the AMCAS application and fill out most of it (i believe you need to write institutional information), you will get an option to print for transcript request. Print that out and highlight the important directions you want the registrar to follow. Those will go straight to AMCAS - not the individual medical schools. Personally, I suggest that you get your transcripts in ASAP (as soon as you can get the form printed out from the application). This way, you can continue to work on ur application while your transcripts are being sent over. By the time you get done, your transcripts will be there and your file will be complete.
I know of some people that sent out their primary, then filed for the transcripts which delayed the application another month - so definitely get that in ASAP