I've done the bow thruster thing, so this isn't hypothetical, it's real world.
Island Breeze is a 56 footer that weighs 26 tons and needs help in tight spots, so the boss decided to install a thruster.
We went with the biggest DC thruster on the market at the time. It's a 13 inch, 24V Vetus.
Since that's the only thing on the boat that operates on 24 volts, we decided on another bank of batteries dedicated to the thruster. They're mounted right next to the thruster, in the watertight forecastle area. DO NOT USE deep cycle batteries for a thruster! A bow thruster is like a starter motor. Lots of RPM, lots of torque, for a very short time. Deep cycle batteries don't like that at all, just the same as starting batteries don't like little loads for extended times. It has to do with the physical qualities of the lead plates in the batteries.
Anyway, put a battery (Batteries? 24 VDC is better!) forward, but try and find a way to remove an equal amount of weight from up there or the boat will start plunging and porpoising. Remember that when you put the thruster tube in, you're removing some of the designed ability to float from the bow. Now add the weight of the motor, gear head, etc, and you've put a bunch of weight up there. We were lucky. Breeze had a bunch of lead ballast bars to put her on her design water line. We put in the thruster and batteries, then, after the yard dropped her back in the water, we added ballast until she was floating right again.
If you don't have that luxury, you may sit a little bow-down. When going to weather, the boat is going to want to stick her nose in the water because of the lost flotation.
Next, you can remove the wiring from your main house bank to the windlass, and connect them to the thruster battery (batteries), because they're the same as the thruster: lot of RPM, lots of torque for a reasonably short time. You'll be surprised (pleasantly, I might add) at how much better the windlass operates.
As to charging, we have a dedicated charger since we have two 12 volt banks of two batteries each wired in series to give us 24volts. You don't say how big your boat is, but it's obviously not a Cal 24 or something. If you tie to shore power, a second charger is no big deal.
On Breeze, the thruster bank of batteries is completely isolated from everything else. The thruster case is tied to the bonding system, but otherwise has no electrical connection to anything else on the boat.
We've never had to do it, but that means if you run your starter bank and both house banks down, you still have batteries aboard to get your engine/genset going again. It might be a pain, but it will work.
As to the suggestion of using the windlass power, I'd be leery of it. You don't say who put the windlass in, but if you did, and followed the manufacturer's guidelines, your wiring is probably on the wrong side of being heavy enough. If a yard did it, you can bet your last dollar they scrimped and maybe went a size too small.
Rule of thumb: run the device for fifteen seconds. If the wiring is warm or worse, HOT, the wiring is too small.
On Breeze, the longest cable is about four feet long, and I used 3-0 cable. The factory said I could use single 0 cable. Sorry. The thing is fused for 355 amps. I'm not going to run 355 amps through single ought cable.
If you decide on going 24v, but don't know how, ask, and we'll exchange emails or phone numbers and I'll talk you through it. No black magic involved.
S/V Island Breeze