Hi,
I would go with twin banks. I use switches from Napa so I can use one bank while charging the other, or turn them both off, or use them together.
Napa DC switchYou must fuse of course.
If the compartments are big enough and your pockets are deep enough 8 D might be better than group 31 as then you don't have as many cells to deal with.
I'd go with poly solar panels and lean towards the 500 watt mark. Of late, high voltage panels have become less than $1.00 per watt so MPPT controllers are beginning to make sense again.
Here is a place to look at panels:
Solar Blvd
