how to record prepayments for assets or Pro-forma invoices

we frequently need to make wire payments in advance of receiving an invoice, non-inventory items. We record the wire as a manual check.  We have had duplicate payments to vendors as we've lost invoice # being the control.  When I view the vendor inquiry invoice tab it appears we have an invoice "MC & date" that offsets the payment when we should show an overpayment to the vendor.  are we missing a box that needs to be checked?