I always clean my knives first, and I've hardly used the brown stones, I keep my knives sharp by a few regular strokes on the whites. I was trying to restore an edge on a friends knife that had gotten too dull and had a hard time. I thought I was a great sharpening whizz because my knives are so sharp but I guess it's just cause I havn't let them get dull in a long time.
When I used the brown stones on that dull knife they didn't seem to work any better than the white ones, I wound up using alternative means and finished up with the whites on the sharpmaker. I keep my stones pretty clean, the brown ones just never seem to get that way.