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....not sure how one could get them running on a separate battery and taking orders from the Arduino...
I'll probably also throw in a few transistors here and there to make sure things don't go boom.
Would it make sense to put a large capacitor after the fuse to regulate the current? Or would that be counter productive?
We've planned to use a laptop on the surface that'll be running a program/as well as showing video.
First off, the battery. My suggestion would be a Hobby Li-poly battery like This One. The reasons are they are cheap, and support large currents. You mentioned you are using bilge pumps, which can draw large currents. I know the 12V one I have for my saltwater change system can draw 3-4Amps under load. So worst case for you, 3 pumps at full load would be 9-12 Amps, which other battery types would have a hard time sourcing. However, they can be dangerous, and you should definitely have a something like a 15Amp fuse in-between your battery and ROV electronics.
I'm having difficulty finding a good charger for this battery