Pre-Payments to Suppliers are created following the steps illustrated below.

From the Bills window of a Supplier click the 'New Payment' icon. For a pre-payment that is not associated with any existing Bill just click the 'New Payment' icon in the lower right corner.

The next screen you will see will be the payment screen.  Choose the Type of Payment(The Types are editable based on User Access Settings through the Blue plus on the right side of the field), type in the amount of the Payment. The payment amount will pop up in the fields at the bottom of the screen.

Click the Save icon in the lower right when you have finished entering your payment information.

Since this is a Pre-payment it will be shown in the next screen as a pre-payment.

As future Bills are added you will be prompted to allocate part or all of this pre-payment to current Bills until the balance is used up. If there is a difference between a future Bill and a Pre-payment then when you click the print box when you Save the Check that will pop-up will take this into account and print out any difference between the two.