This is not possible in GP. Here is the answer from Microsoft on it:
Since these are multicurrency documents, you must first post the manual payment before you are able to apply the payment to the invoice. You will not be able to apply the payment to the invoice on the Manual Payment Entry window.
Multicurrency transactions require a 3 step process to apply transactions entered in a currency other than your functional currency. The 3 step process is:
1. Post the invoice.
2. Post the payment.
3. Apply the payment to the invoice.
If you want to keep applying manual payments for functional currencies, you can take these steps:
1. Check the Apply Manual Payments checkbox in the Advanced Settings
2. Run the Payment Confirmations in the connector (the functional currency payments will succeed. The non-functional ones will fail)
3. Uncheck the Apply Manual Payments checkbox in the Advanced Settings
4. Rerun the Payment Confirmations (The non-functional confirmations will come in as loose payments)
5. Post and apply the non-functional confirmations using the GP tools