Under Returns filed on the Sales tax report, choose Record return with the period, the date you filed and an optional reference. Magpie keeps the figures and posts an entry on the period's last day that sets the recoverable tax against the tax charged, so Sales tax payable holds what is owed. Add the payment from the bank against Sales tax payable.
Close the books through the end of the period is on by default, so the figures you filed cannot change. Periods cannot overlap, and Remove reverses a return's entry. Magpie records returns; it does not file them.