Some schools requires you to send the secondary/supplemental fees "at the same time" when you submitted your Aadsas application.
There are schools that have their secondary application ready like creighton university, u penn and marquette. You can check the "participating schools" section in the aadsas.adea.org. The schools tell you what to do. Also check the website of the schools that you are applying to.
What I did was as soon as I e-submitted my application. I mailed the checks / money orders that the school requires. I also turned in the secondary papers for some schools.
However, some schools asks you to wait till they "contact" you for you to send the secondary papers and fees. USually they contact you through your email.
hope this helps a bit