Personally I would keep one of the batteries connected/active to keep the voltage stable when starting motors like the tks pump.
Pre-DX (2004) ovations do not have a true dual bus setup so the emergency bus is really just a way to quickly reduce the load without going unit by unit.
Probably the old emergency bus had the backup vacuum pump so you probably have amps to spare.
More important questions for an all electric panel IMO:
Do you check the batteries every year for reserve capacity?
Have you tested the backup alternator for proper operation under load and has it been rebuilt / inspected lately? Its spinning every time the motor is on...
To me the backup systems on the ovation buys me time. Personally the only time I would hit the emergency switch is if I was really in the thick of it. Otherwise I would shed the load until the backup alternator was able power what was remaining (very easy to observe on the amp meter). This means the AP, GPS, etc.