Hi,

For this, here is what you could do:

1. Simply make a supplier payment without selecting an accounts payable record to pay against.
2. This should make the Difference Amount at the bottom the same as the deposit amount.
3. Leave the Payment Difference as 'Keep Open'.
4. Validate the payment and a journal entry should be generated with accounts payable (on the debit side) as a contra-account to the bank account.
5. When you receive a supplier invoice, accounts payable should be created with the full amount.
6. When you make payment to the supplier, select and reconcile both accounts payable records from 4. and 5. to proceed with payment of the remaining balance.