The key people worked with to set this up were Bob Arasmith (developer of webyouthsoccer site) along with Owen Gan and Araceli Cardenas at the AYSO National Accounting Program. They are the official ones that own the AYSO Paypal account.
Instructions from Bob (8/2/12):
First you need to contact national, assuming you have a paypal account through them, and have them turn on your Instant Payment Notification (IPN).
It should point to https://r64.webyouthsoccer.com/payment/ipn_receiver.php
What this does is notify WYS when someone pays via paypal.
Then you need to construct two static webpages;
1. A page that the parent lands on after a successful payment, maybe describing when to expect the coach to call, thanking them, etc.
2. A page that the parent lands on when the payment was cancelled, maybe telling them other methods to pay.
Then you go into WYS and visit the Admin > Registration Opts page where you configure your paypal options in WYS.
Do not enable it until everything is configured properly or you will deadend parents.
Three of our pages are critical to make this work:
Transactions for paypal payment appears on parent's credit card statements as "AYSO R64"