whoa...good thing you came on sdn.
so you have your primary application (AMCAS) - includes:
personal statement
activities
classes you have taken with their grades
schools you wish to apply to
now secondary applications are the applications given to you by the schools you designated. if you do not qualify or pass the screen at some schools you will not get their secondary application and thus that is a basic rejection.
but for the ones you get....you fill them out, most have questions you will write short essay responses for...and whatever information they want...and you send it back to them. at this time you send your LORs to them as well.
schools then look at both primary and secondary app...and assess if you should get an interview and so on and so forth.