The easiest way would be to run a wire from the clock to the "always hot" side of the cutoff switch.
On the Mini I have a battery cable disconnect. I have a 5 Amp fuse wired in parallel to the disconnect. That allows me to keep the low current items running with the battery "disconnected". However, if someone were to try and start the car with the battery disconnected, the 5 Amp fuse would blow. So... I still have an anti-theft disconnect while the accessories can still be powered up.