It is common practice to flatten water stones with a piece of sandpaper and glass or any flat surface. The glass, unlike your table saw, wont rust while keeping the sandpaper wet. This just prevents clogging and tearing of the sand paper. It is also common practice, and recommended to keep whetstones submerged, unless there is a possibillity of the water freezing. This will definetly break up the stone. Technically, wetting and drying a lot will degrade whetstones. Its basically a form of water errosion, but keep in mind this is such a subtle process that it probably wont effect the life of your stones if used occassionally.
I finally broke down and bought some DMT 8'' x 3'' Diasharp steel sharpeners in extra coarse, coarse, fine, and extra fine. These stone have a lot of advantages like, they never cup, they can sharpen higher grades of steel with ease, the corners dont round, and they are amazing at sharpening wide things like plane and chisel blades. They also have some disadvantages like being expensive as hell, heavy(not an issue for bench use, but wears your wrist out sharpening a pocket knife), and they are very thin. You need to set them up on something to use them on a bench.