Like Josh, lap my stones after each use. That way I can always start my next honing session with a flat hone. When I am removing nicks on my norton 1000 / 4000 I sometimes lap in between too.

Think of it like this: if you lap after each use, you only need to remove a tiny bit of material, so it will be done very quickly. If you wait, you need to spend a lot more time.
I heartily recommend using a flattening stone.

They are a lot quicker than the sandpaper, a lot less messy, and easier to use.
The norton flattening stone costs 30$, and in bang per buck it was the best investment I ever made for honing.

Currently I am using a DMT 325 grit (55$). It cuts a bit slower, but the diamond plate can also handle all other types of stone without problems.