This is actually a pretty straight-forward feature.
When creating lines in the Payment journal under Accounts receivable, make sure that all lines have Use a deposit slip checked.
Then once the journal is posted, under Functions you will find a Deposit slip option. What this feature basically does is collapse all of the Bank transaction records generated by the journal into a single Bank transaction, and move the original transactions off into a separate table where they can be accessed under Cash and bank management, Deposit slips. Then during the next Bank reconciliation process, the single transaction should match what appears on the bank statement for that deposit.
Hope this helps.