I may be wrong, lord knows i often am. My thinking is that if you run a positive from a good battery but do not tie the grounds together in the boat you will not start the motor. I am assumeing the trolling motor battries are stand alone and not grounded to the boat system in any way. Think about jumping a car off. two sepetate systems. just running the positive will not do anything. you have to ground the good system to the dead batter of the ground system on that car.
As far as taking 12 volts from 24 volt system, yes simply run the positive and negative off one 12 volt battery and the fact that it is tied into the 24 volt pack will not matter.