Josh, you got options - a bunch of them! Depending on which isolator you are using, you could probably just replace your small current auxiliary battery with a larger marine (of which there are several types) battery. As Larry said, if you are running your batteries in parallel, they should be the same size and type batteries. This is because the batteries will equalize themselves so a larger battery will be limited to the capacity of the smaller or weaker battery. However, most automatic isolators have diodes in them that keep the batteries from "seeing" each other. Therefore, you can, for example, have a small battery (like the OEM) as your main battery and have a much larger, deep cycle, as your auxiliary battery. The diodes in the isolator keep the batteries from trying to equalize therefore allowing the aux to charge to it's full capacity. In a dual battery setup, the main battery doesn't need to be very big at all, it's function is to start the engine, run the stock electronics and the headlights, period. That type of battery is called an SLI (Starting, Lights, Ignition), most cars use the same 'type' of battery, different sizes of course. (As a dual battery user, you probably know all this, but for the benefit of others, I'll ramble on.) Off the showroom floor, that is all the battery you'll ever need. The rub comes when we, the end users, decide to add extras like light bars, radios, maga amplifiers, gillion pound winches, refrigerators, 60" TVs... you get the gist! We soon exceed the designed capacity of the stock electrical system so we add more capacity in the form of an additional battery. There are a bunch of ways we can add that capacity. Probably the two most used approaches are to either run the second in parallel, or putting an isolator between the original battery and new, second battery. Both approaches effectively double the electrical storage capacity. Truth be told, 95+% of the time, a parallel setup is probably all you'll ever need but, as Larry outlined, the isolator setup adds a couple of advantages. First, the main or original battery is protected from being drained by your accessories thus ensuring that you'll always have the battery power to start your engine and get you back home. A second advantage is, as noted above, your auxiliary battery can, if you choose, have a much larger capacity than the original battery allowing you to run your accessories longer, especially if you run those accessories with the motor off. Oh, by the way, there is another reason to have a second battery, backup, in case one battery fails!
Now, back to your situation, use the better of your two existing batteries as your 'main' battery. Buy a big ole honkin' deep cycle battery to be your auxiliary. Hook your isolator up between the two. Leave your other where it is under the hood, with no connections and fully charged and when someone in your group who doesn't have your wisdom or foresight, looses his battery, loan him your extra. Polaris people being the standup, upper class citizens they are, will surely write you a large check out of gratitude for bailing them out! :smug: