On your pending vendor invoice, when you view the header information, you will find the button "Prepayment". The help text of this button is as follows:

"Select this option to indicate this invoice is a prepayment. If this option is selected, the options in the Purchase order field include only the purchase orders that have a prepayment remaining amount for the selected vendor. This field is not available if the selected purchase order does not have a prepayment remaining amount, or if a prepayment has not been created for the purchase order".

Anyways, you are currently not able to set this button to Yes because it is completely deactivated. The only possibility to create a prepayment invoice for a purchase order is from the purchase order. If you get your invoices from invoice capture for example, you are not able to declare them as prepayment invoice anymore.