It is a good idea but I would not use the cranking battery for trolling motor unless it is a deep cycle like your trolling battery. If it is still not good idea to run down cranker. I would get another troller with a few dollars more than your perko switch. Hook your 2 Trollers together positive to positive, negative to negative. Hook charger to one and charge both at same time. Every now and then after charger kicks off let battery settle for hour or so and disconnect one if you have a meter and check voltage on both just to make sure they are both toping off.
I have never found a switch that would carry the load of trolling motor any smaller than the Perko if that is the direction you decide to go. Good luck which ever way you go
Proud Member of Team Geezer
Charlie Weaver USN/ENC 1965-1979