atom,
Well actually your battery should power your 12v cicuits, your solar controller will keep the battery charged as well as it can, then you just sense when your battery gets below 50% State Of Charge to determine if the generator needs to run. A 3-stage RV converter will be the most economical charger for long term running, but you maybe could find a heavy duty charger elsewhere that will "pump" more in faster. No need to disconnect one when charging with the other.
Actually, voltage measurement is a very poor way to determine battery SOC, total amp hours in and amp hours out of the battery will tell you a lot more accurately, check out Hall Effect sensors or "shunts" for the Arduino.
It sounds like all of you need a lot of education on solar power and "off grid" living, check out these forums
http://www.wind-sun.com/ForumVB/index.php
or Google for sites
Here, for some easy to understand info The RV BATTERY CHARGING PUZZLE « HandyBob's Blog
Didn't mean to be condescending, but after 40+ years in electrical and electronics, I was amazed at how wrong I was about a lot of solar info, and how little I actually knew.
Your brain will hurt! There is a lot of info out there, make sure it is right by double checking as many places as you can. Some sites are only interested in selling their stuff, others have no actual knowledge of electronics, some both.
Spend a little more for reliable equipment, you'll never be sorry.