You can register prepayments by using New Sales Receipt (Sales - More - Sales Receipts - New Sales Receipt).

Example: you receive a €500 prepayment for which you will issue a €1000 invoice

1/Partial Invoice

Creating a €500 prepayment receipt:

Click "Print". You will see that the receipt is marked "Prepayment Receipt". The payment type is clearly indicated. Several different payment types, such as check or card, are authorized. 

Note: an invoice has not yet been generated.

2/Invoice with Prepayment
Creating an invoice registering a €1000 sale:

You will find the "Allocate a payment deposit" button on on page 2 of the invoice, which works similarly to the Receive Customer Payment screen, enabling you to retrieve and assign the €500 prepayment as soon as you create the invoice. 

This button also enables you to allocate payment deposits directly from the invoice. 

The invoice thus shows all the correct information related to the prepayment.