My other boat is a pontoon

So, I was all done winterizing my pontoon equipped with two 12V batteries hooked up to a Suzuki DF140. I disconnected the positive cable from the first battery...before you could say oh snap, the smoke was coming up from 2 small wires at the very bottom of the lower unit. I unhooked the negative ground from the battery and that stopped the smoking...no doubt I caused a short or something. I ended up taking off the other battery as well and now wonder, what did I damage if anything? Any experts out there, please holler...thanx!