My new Ranger Z520 has a battery switch very similar to what ToadThrower posted that allow the battery selection of the 1st, 2nd, 1st & 2nd (Jump), or none. The only thing I was told to watch was to ensure I did not have the jump mode selected when I plugged in the charger. My boat has a 4 bank charger so both batteries are on separate charger banks. So I don't think there are any issues with running the motor in dual battery mode or Ranger would have some caution in the manual.
Ranger Z520 and Lance 825
My second homes :-)