For chisel ground edges, just sharpen the one side till it forms a very small burr on the flat side, then wipe the flat side "edge" at a very low angle with a fine or super-fine hone of some sort to knock the burr off. Maintaining a perfectly flat edge is something that usually isn't required (or even wanted in many cases) on the blades most of us carry from day to day. A benchstone + human limitation, combined with the extremely narrow bevel of a knife usually results in a very slightly convex edge, which is a very good for using knives, as you can get it easily as sharp as a perfectly flat edge, but the edge geometry is stronger, which generally aids edge holding in hard use situations. If you want a thinner edge then just lower the angle a bit.
If absolute flatness is your goal, on a knife you'll most likely need to use a guide/clamp system of some sort, such as the edgepro Apex or a Lansky setup. On some of my smaller pocketknives I've used the lansky and the coarse stone to do initial reprofiling, then finish on a benchstone. The coarse stones dish out and are difficult to keep flat, so when you move to a higher grit it's easier to match the angle by hand sharpening as opposed to the finer lansky grits. The coarse and medium diamond lansky stones are probably a good investment if you use it to reprofile your edges. The edgepro I've heard (but never used unfortunately, I'd like to try it out as I love having perfect edge bevels on gent's knives, they just look cleaner) is the best way to get perfectly flat edges on cutlery.
On actual woodworking tools like chisels and hand plane blades the long wide bevel is easy enough to keep flat on the stone. Waterstones work great for these tools as they glide over the hone and tend to "stick" to the surface which helps keep the tool flat. You'll want to keep the stone as flat as possible with a lapping plate so that as you progress in grits you always have a matching flat surface between the tool and the stone.
