Bank deposit question

I have a bank deposit ($1,000.00).  Of that amount, $600 is a payment from a customer, while the $400 is reducing a current Liability (Due To XXXX).


How do I get this to show as only the $1,000 deposit in the bank general ledger?  Up till now I have been doing separate entries for these types of things then having to reconcile these at the end of month when doing my bank rec.