Long reach paint pad keeps tight spots neat. If you have a tight spot to paint, remove the pad from a paint edging tool (about $2 at home centers). Hot-glue the pad to a stir stick, and you've got a painting tool that will fit behind toilet tanks and radiators.
The only sure way to keep water from reaching the backer board is to waterproof all areas that may be exposed to water. That's easy with the new waterproofing coatings (RedGuard is one brand). If you're in doubt about potential water problems, coat the area with waterproofing. Follow the application instructions on the container. You can apply it with an inexpensive paint pad, which allows you to quickly spread a thick, even layer. You can also use a brush or roller.