What you do would be to use the New button, then select bank deposit. Your undeposited transactions that are still in the undeposited funds account should show up as ready to deposit. Then put in the deposit date, and choose the bank account, then select which transactions to deposit. If cash is also being deposited, it can be added down below.
Another way to view the undeposited funds account (though it is not efficient for grouping anything together) is to go to the register of any of your bank accounts, then switch the bank to "Undeposited funds". Alternatively, you can pull up the chart of accounts and open the undeposited funds account from there. This will show the complete transaction history of the undeposited funds account.
