RE: prepayment without purchase order
Without prepayment Invoice
If you need to accept an advance payment without a PO or an Invoice, you can do it in the payment journal, post the payment without applying. You can later apply that payment to the respective invoice, once the invoice is created in the system.
Vendor will have a debit balance, because of the advance payment until you create the invoice for them.
Creating the prepayment invoice manually.
If you need to create a prepayment invoice without a purchase order, you would have to manually create an invoice in the system, by selecting the prepayment account, and then you can post the payment (deposit) against that invoice.
Later when you create the actual invoice, you'll have to manually add the prepayment account to the invoice lines and deduct the deposit amount by adding it as a negative value.
Simply what you're doing is creating the prepayment process manually, because you didn't had a PO to create the prepayment invoice at the point of receiving the deposit.