Apply book transfer as payment on A/R invoice

Currently, if Client A is making payment on vendor Client B's A/R invoice by book transfer and Client B's deposit is being automatically being recorded, the payment is not being applied to the invoice. We have to make a separate deposit entry on Client B if we want to apply the payment to an A/R invoice. It would be nice to be able to apply Client A's payment to a selected invoice of Client B's and automatically record Client B's deposit with one entry.