AccountRight Premier - Apply deposit paid into multiple invoices

Hi

1. What is the best way to Apply deposit paid into multiple invoices?

Currently, I created an order and paid a deposit to supplier.

When the supplier's bill is received, I applied partly deposit from the now converted order in a bill, with a NIL amount, so that the deposit amount is on Negative balance.

2. This causes an issue from doing BAS cash basis, as the deposit paid is not being recognised as it has a blank bill. 

Can you please advise if its a faulty on MYOB or provide suggestion?

Thanks

Thierry