Since they are 24 volts you must size the batteries so they have sufficient capacity to do all the desired tasks without relying on help from the engine
alternators or line charger
. Estimate (or measure) average current
drawn and multiply by the worst case time they will have to run (in hours) to get an amp-hour rating. For good battery
life you should not discharge below 50%, especially in 24 volt systems so double the number to get the minimum needed battery
capacity. Any increase over that will more than pay for itself in extended battery life if you have the space and weight is OK.
If you run the genset normally when underway a 2 bank charger
will recharage the batteries.
A Trollbridge24 would charge the batteries from a 12 volt line coming from the starting battery but you are correct, you would not be able to run the windlass
and the thruster at the same time without overloading it.
I've never used one but I understand there are some 12 to 24 volt voltage doubler converters you can use to charge the 24 volt battery. Since they just double the incoming voltage you don't need a regulator
because the 12 volt supply is already being regulated.