Will not work because the trolling motor battery`s and the cranking battery uses a separate ground. You would have mount 2 separate switch`s. Just a suggestion keep the jumper cables in a water proof container. I don`t know how many times I have seen booster cables that look like they have been laying on the bottom of the lake. Useless.
Why can't you connect the starting battery to the first trolling motor battery in a 24V or a 36V string? I have a 24V system and my lights and electronics are running off the positive post on the first battery which provides 12V and shares a common ground with the starting battery.
Which brings me to another question. Is there a reason to not have the starting battery and the one supplying 12V to the boat's systems on the same ground? When had a 12V TM, I installed a Blue Sea ACR and the installation diagram showed the starting and "house" battery using a common ground. That should be OK with my current system as long as it's the 12V sources sharing the ground.