I hate to keep asking questions buuuutt ... Do you know which kicker sub?

I'm assuming the in-boats are the factory kicker in-boats. I think the goal there would be to get them in the 50 watt rms range. Then you want enough amp (if going with option #1) to give the sub at least 300rms, I'd think.

For hypothetical purposes, lets say you get the JL XD700.5 (you would be looking for something similar). Option 1 that was discussed before would look like this:
In boats: 700.5 using 2 channels to bow and 2 channels to cockpit = 2 x 60 watts and 4 x 45 watts
Sub: 700.5 using the sub channel to give you 300 x 1
Tower: factory amp bridged giving you 200 x 2.

That gives each of the speakers what they are looking for and will sound exponentially better than 200/9, which honestly, I'd be surprised if all speakers were running if they are all hooked up to the amp.

End min goal should be: min of 75x2 to tower; min of 40x6 (likely in a 4 channel setup)to in-boats; min of 250x1 to sub
End ideal goal should be: 100x2 to tower; 55x6 to in-boat; 300+ to sub.

Don't let the second battery scare you from an install standpoint. It's not bad.