When you pay more than the balance due on an account you should use the Payable Payment option to record payment of the payable (but only enter up to the balance of the payable in this box). Next use the Purchase Option for Other Assets and setup an other asset with a name such as "Overpayment of Account." Enter the amount that you are overpaying by. Also be sure to select an offsetting expense account. This is the expense account that the payment will be applied to on your cash books. When you later use this overpayment for a future purchase, you can go to the other asset purchase box again and select the account and enter a negative to show the use of the amount.
Note that if you ever do any prepaids, you can use the other assets in the exact same manner for setting up prepaids (your manual has a good explanation of setting up and using prepaids on page 276).