It looks like I am not able to create a cheque for the balance of a vendor bill with the "Pay via Check" option, for a bill on which I had already sent a pre-payment amount via an EFT.

For example, if my credit limit for a vendor is 50K and my order is for 75K. The vendor will ask for an advance payment of 25K before releasing the order, so I did this and created the corresponding payment. But once the official bill becomes due, it would be nice to be able to create a cheque for the 50K balance.