Prepayments may be collected and deposited even as early as the quote level; they may also be collected at the order level before an invoice is generated. This will (depending on your G/L transaction mappings for A/R and unapplied cash) debit a cash account and credit a prepaid account.

Then, once the final invoice has been generated, any prepayments that were processed on that particular order, their prepaid accounts will clear instead of the balance that would have normally been put toward A/R (unapplied cash generated from the initial prepayment will auto-apply). The balance amount will be left on the customer account as A/R to be collected per normal collections process.