Re: Switching batteries to start the motor.
The only advantage to using the "both" position is the extra cranking amps as amps are additive and volts divide.
It's very possible that a battery can show 12.6v and yet have no amps to crank.
Therefore, use the designated starting battery to start - unless it won't, then switch to both, start and leave it there to charge (i.e., leave it on both to charge because something is wrong with the start - that way if the start is dead you can at least get something into the house while trying to charge the start).
Only turn the switch while the engine is running if you have a "make before break" type switch.
Lessons learned are opportunities earned.