I'll help you take care of those deposits and shed some light on the Undeposited Funds account.
To clarify, the deposits or payments in the Bank deposit screen are already in the Undeposited Funds account. They are just waiting to be deposited to the bank account.
When you receive payments from invoices or process a sales receipt, there will be an option to deposit the funds to the bank or the Undeposited Funds account.
It's likely that the Undeposited Funds account is selected under the Deposit To drop-down menu. When you receive your payments, ensure that the bank account is selected instead.