Here is the deal. You can switch between bateries while running only if your switch is make before break. The vast majority of switches are this. But I guess if you don't know then you should find out before you do it. Don't turn to off while you are runing. switch from 1 to both to 2, or vice versa. never to off. Never run on both.
To wire the boat for two batteries is quite simple. Wire ground of Batt 1 to ground of Batt 2. Run hot of batt 1 to switch. Run hot of batt 2 to switch. run hot off switch to outboard. run ground of batt 1 to outboard. run hot off switch to house. run ground off batt 2 to house. DONE. very easy. I did it in my last boat. I have done it in 4 friends boats. It is tooo easy. I just bought supplies to do it in my brand new boat.
I prefer the Blue Seas switch. I use #2 AWG wire for the long runs and #4 for the short runs. I have never done a boat bigger than 21'. I may use larger gauge for a bigger boat, I would have to do the calculations.
I have found the best prices at
www.bestboatwire.com. About 1/4 the price of west marine.