Personally I don't worry a great deal about dishing of stones when they only get used for knives, but here's how I'd flatten a waterstone. Scribble over the surface with a pencil, tape a piece of the roughest sandpaper available to a flat surface. (Part of a defunct cloth backed sanding belt is good, on a machine table, but a piece of thick glass is just fine). Bear down heavily and rub back and forth until the pencil marks have disappeared. Repeat with finer paper until it's as you want it. If the stone is a hard one like an Arkansas, this will be a long sweaty job.
For a new stone, I'd suggest a fine diamond plate, or better a coarse / extra fine combination one. Try dishing that!