I usually lap my stones after each 1-2 knives. The flatter they are, they better they will perform. I usually use a diamond plate - either the WEPS stock diamonds or a full size plate.
Rubbing the stones together does help in the short run, but should be monitored over time, with occasional lapping on a flat surface to true them. Rubbing the 2 flat stones together to form a slurry is good for a more aggressive stone. I don't recommend it past the 1K or 2K stone, though.
Leaving dried mud on the stone (black in color) is not really advantageous since it will slow down the action of the stone on the next knife. If you are just touching up, then leaving the mud can be helpful. You'll need to play with it to see if it works for you.
Here's a Chosera lapping tutorial I did a while back: