Depends: if the oem thermostat requires any kind of intervention to restore function following a power fail, then you'd need to remove or bypass it and let the external controller run everything.
Otherwise, if it behaves itself and acts like an old-school mechanical thermostat that just picks up where it left off once power returns, you can likely leave it in place set to its lowest temperature and, again, let the external controller run everything...
Cheers!