When we travel back roads we look for major highways that intersect, like US highways and interstate highways, then we locate a truck stop near the intersect point and go a bit out of our way for fuel, then return to the back roads.
The only place I know of where you can get low clearance info is in the Motor Carriers Atlas (Rand McNally makes one). Not sure if it gives enough detail for back roads. They usually just give the truck route info. The Rand McNally GPS does warn for low clearance, however for back road travels I'm not certain a GPS would work. You usually have 2 route options, fastest or shortest distance.