I know a lot of people on here fish so I’m asking here as well. I can’t get my head wrapped around how to use a multi bank charger. I have 24v trolling motor and then boat runs off 12v. Is there a way to charge both at the same time without having to separate the trolling motor batteries every time or will i need to have to separate bank charges one for 12v and one for 24v?
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The multi-bank are all isolated and therefore there is no shared ground reference, so each bank output has it's own isolated positive and negative connections that connects to the positive and negative of each battery. The charger only cares about the voltage difference between the positive and negative of the battery on each bank output, and charges each battery according to that. So it's really like having multiple chargers in the same box, but isolated from each other.
Because of that, you don't have to disconnect any battery cables, or remove bus wires that connect two batteries in series for a 24V bank, etc. The common type for a 24V trolling setup is a 3-bank charger, and a 4-bank charger for a 36V trolling setup (or for a 24V trolling with 2 starting batteries).
Don't really worry too much about charger output amperage, as you'll have plenty of time to charge everything if you're not taking the boat out every day. The higher amperage multi-bank stuff (15A per bank or whatever) are mostly geared towards people like tournament fishermen who need to charge overnight and be back on the water the next day. If you get something like a 10A per bank, it just takes longer. That's why you often see "Tournament" or "Professional" in the names of the 15A per bank stuff, and "Sportsman" in the names of 5A or 10A per bank stuff.
Let me save you some shopping time: Buy one from Hodges Marine; they usually have about the best prices you're going to find anywhere.
They carry Dual Pro, Minn Kota, NOCO, and Pro Mariner, and those are really the only brands worth looking at for a fishing boat.
Marine On-Board Battery Chargers Portable Boat Power Inverters