There are better battery experts on this forum than me, but I'll start by asking if either one is a Deep-cycle battery? That would make sense for the stereo. And which ever has the highest Cold Cranking Amps (CCA) would be best for starting the engine.

I wouldn't be surprised if your boat was set up with the group 27 as a starting battery and the group 31 as a deep cycle battery, but check the labels and see.

Do not use a deep cycle battery as a starting battery if you have a modern electronic engine. Meaning it is not a carburetor engine. I don't see boat specs on your questions.
Per the volvo manual for the model I have they state not to use a deep cycle because they do not provide enough amps while cranking and could fry the computer. I would imagine pretty similar for merc...
So as rpengr stated use deep cycle for stereo and cranking battery for engine. Bigger is always better in batteries. The other option is "dual purpose" batteries which are supposed to be right in the middle for boats so you can use it for cranking the engine and a little deep cycling. Not intended for a trolling motor but for a stereo it should work okay.
Others will have a better idea on the drain of a 2k amp and could probably recommend a more specific battery or maybe even needing 2 for the stereo. Sounds like a pretty large amp.