Recomendation on batteries?

[tower]

Nope! Taz, for running accessory loads with the motor off, you definiely want the yellow top. Though slightly costlier than the red top, the yellow top is a deep cycle battery, designed to be run down and recharged repeatedly.

There are severl good isolators on the market. There is one coming out soon with extremely low draw, but it is a month or 2 away from release. For now, any battery management system, for example http://www.hellroaring.com/rv.htm
will work for your purposes. I have used yellow tops in the most extreme environments and run them to "dead" status many times. They have always charged right back up and operated like new and still always supplied more than enough cold craning amps to get me going.