I don't see why you don't want to tie the batteries together in parallel? That way at least while the outboard is running it will be charging both of them unless it has no charging circuit...I have a 10 hp outboard electric start with it's own starter battery and a separate house battery. My house loads are fairly modest as I only have running lights, radios, and a few cabin lights. I have no need to switch the batteries together as far as I can tell. Question is: if I use 6 AWG battery cables, how do I run the positive to the positive end of the panel. there is no + bar on the panel only 16AWG leads on the positive and 16 AWG leads jumping from neg to neg...
You need to also fuse those batteries. I use...

...the above on the Mac with 60 amp fuses and #4 wire which is fine for my highest load which is the outboard starting.
On the Endeavour with higher starting loads I'm using...

http://www.defender.com/product.jsp?path=-1|328|296553|319682&id=1334570
...the above that go on the battery pos. post and are easier to install than what I used on the Mac.
I have more on the Mac wiring here....
http://purplesagetradingpost.com/sumner/macgregor2/inside-30.html
...which would be pretty comparable to what you are doing with the exception that I also have input from a gen-set and solar panels which you could ignore. You will see...

.... Pos. and Neg. posts in the link and above that are connected to the batteries and also a shunt for an amp meter. You could come off of the posts to your panel with #10 for your loads.
Here is a good source for marine wiring that I use...
http://genuinedealz.com/
Good luck,
Sum
[FONT=Arial, sans-serif]============================[/FONT]
Our Endeavour 37
Our MacGregor 26-S Pages
Our Trips to Utah, Idaho, Canada, Florida
Mac-Venture Links