Required prereqs should come before the application. You can/should complete everything on you AMCAS app...personal statement...experiences...bio info...and all grades in the courses you've completed so that when your summer classes are done that's all you have left to enter. Send your transcripts immediately (as soon as they as available)!!! I submitted my app in Mid-August. It was verified in about a week.
Are the summer courses at a different institution than your undergrad institution?
Are you taking course this spring?
Do you know who your letters of recommendation are coming from?
Are you using your school's premed advisory committee?
Send Supporting Documents to Schools EARLY
Complete Secondaries EARLY