Sorry I did not understand the question completely.
There for usually two ways to handle prepayments.
1) When you make a prepayment you book it as an asset (lets say $100). When you receive an invoice (say for amount $20) you apply the prepayment. Prepayment entries are reversed and invoice expense comes into the picture. In other words you transfer the amount from prepayment asset to the invoice expense ($20). $80 are still remaining in your prepayment asset. They will be converted to expense when the prepayment is applied to future invoices.
2) You book prepayment amount (say $100) as expense because you are hoping to use all of that in the same period. You only received an invoice for $80. $80 was moved from prepayment expense to your invoice expense. Prepayment entries will be reversed by the system when you apply it to the invoice. You must move the remaining $20 into some asset account manually before reports are published. $20 must be represented in your balance sheet as an asset (and not in your income statement as an expense) because it is still an unapplied advanced payment which is conceptually an asset.
I hope that helps