Hi Dave,
If you use a failsafe switch with the SuperReg, it is a single switch that turns the regulator on/off. You are right though that it draws a small amount of current, about 10mAH/day, when in the off position. Using the failsafe switch you also need to mount two charge jacks which we provide for charging the two batteries. You can also check each battery through its respective charge jack.
Let me know if you have any other questions.