To apply customer prepayments to the invoice, click 
(the Edit prepayment offset button) to the right of the Prepayment field at the bottom of the form—this opens the Offset Prepayment dialog box.
The "Invoice Received (create)" form. The Offset Prepayment dialog box
The Offset Prepayments dialog box contains two panes:
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To automatically apply the prepayments to the invoice, click the Auto Fill button. The system selects the documents starting from the earliest ones (by using the first-in first-out rule) until either all the available documents are applied or the amount of the applied documents becomes equal to the invoice amount.
To manually apply a prepayment, select a prepayment in the upper pane and double-click it. Repeat for other documents if needed. Use the Up and Down arrows in the group 
of arrows to rearrange the documents in the lower pane. Then, in the Amount column, you can edit the amounts of the payments that must be applied—the amounts in the upper pane will be adjusted accordingly.
| Note. If any prepayment has been applied to the invoice, on invoice posting, the total VAT amount is recalculated as VAT for the remaining open amount. (Open amount is the invoice amount minus the sum of prepayment amounts). |
The Total Accounts Amount field shows the total applied amount in the currency of the invoice.
Click Cancel if you do not want to apply the selected prepayments. Click OK to save the application of prepayments and close the dialog box.
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