Wouldn't you just leave all the existing equipment connected as is, but, run new cables in series configuration between each battery so only the trolling motor is seeing 24v..
That way the alt can still charge the starting battery. A electronic isolator could be used to make sure the starting battery gets charged first, then the trolling motor battery gets topped up when the starting batt is full.
Depending on the draw from the trolling motor, a 12v to 24v inverter could be used if you don't want to use the starting battery to make the 24v.
If the 2 batteries drop the alternator voltage while charging reducing the charge potential, and the alternator has a reference wire, place a silicon diode in the reference wire to cause a voltage drop to make the alternator increase it's voltage. That way the reg regulates the voltage and when you add a load, the voltage drops, and the alternator can mitigate the voltage drop, to a point, under load.