The quick way to see if you have prepayments is to look at your balance, once you log in to the Resident Center if the balance is negative (in pharentesis) means you have a credit that will be used when a payment is due.
A second way to see the actual prepayments amount is scrolling to the “Account Information” box on the Resident Center homepage and there you will see the “Prepayments”
Any amount paid in excess of what was due will always show as a prepayment until the assessment is due. This will be the case when you pay for the whole year, once every quarter starts you will see the prepayment balance go down as the system is paying itself from your credits.