Follow the directions. If your school interest tells you to send the fee at the same time you submit AADSAS then you should do it at the same time you submit AADSAS. If you have already paid money to AADSAS to process your application, then you have already submitted AADSAS. Typically, DAT scores are requested at the same time that you submit AADSAS.
The other two things AADSAS will do for you is; 1.tell you the date they snail a hardcopy to your schools. This is not the same date they arrive at your school. 2. allow the schools to update your application status so that you can see your status on your AADSAS screen. However, most schools do not do this regularly, reliably, or accurately for some reason. Your best bet to make sure your schools have everything needed for the application is to either read their websites and follow the directions with precision or to read the website and contact the admissions office. Do not call a school without first trying to figure out what they want by reading their publicly available information. Not only do some schools take a while to respond, but you'll feel like an idiot if it is something obvious on their website.
You could alternatively try starting a thread on SDN for your school of interest to see what others are doing that are applying to the same school.
Send your check or money order with your AADSAS # on the comment line. You should also include a cover letter thanking them for considering your application and indicating you are including the requested fees, secondary applications and look forward hearing from them soon. Then put your return address, phone, and AADSAS # as a signature block.