When you receive payments or make sales, unless that money alone is directly deposited, you need to post the payments to Undeposited Funds first, then create a deposit for the date you take the batch of payments to the bank. This account should already be in your Chart of Accounts. You can, in preferences, choose to have this always be the destination for payments.
When ready to deposit you Create Deposit from banking menu and select from the presented payments to mirror the paper deposit ticket you prepared for the bank. Yes, it is one big bulk deposit, as it should be when multiple payments are involved but each payment is listed in the deposit.
If by some odd chance you do not have Undeposited Funds account (I have experienced it missing unless you choose to use it by default) add it now, exactly as spelled as Other Current Asset