Let me help you in sorting things out. If the money is deposited under Undeposited funds when receiving payment your invoice will be showing as paid but not deposited. To change the status to deposited, you need to do a Bank Deposit.
On the left navigation pane, go to New.
Under Others column, select Bank deposit.
Choose the bank account you wish to deposit the payments on the Choose an account drop-down.
In the Received from column, select the invoices by putting a checkmark on the box.
Once done, click Save and close.
To check if the status has changed, go back to the Invoices page and the status should now change to Deposited.