An ATX board is always powered with standby voltage, and then instructs the PSU to turn fully on by grounding a certain wire. Disconnecting the wire again turns the powersupply off (apart from the standby voltage). You'll need to be aware of that mechanism and either bypass it or replicate this fucntionality via someother method if you want the usual auto power off. Alternatively you can power off manually after the shutdown is complete, as was necessary in the old AT days.