The way we do it is to wait for the funds to be downloaded via the bank feed.

On the date of the receipt, select + Bank deposit, split the total payment between the companies. Then go into each customer and create a Receive payment and allocate the Credit Deposit (shown at bottom of screen)  against the relevant invoices. 

The only issue with this is the Deposit shows up as a "Not specified" Product/Service in a Sales by Product/Service report. Not sure why. If somebody knows would appreciate a way around that.