well, cedar shakes cannot be actually cleaned or prepped any way but with a power washer and that can really damage them.
I have found the best way to do this is to actually replace the shakes or the bad ones.
There is a wonder ful paint product put out by the folks at Sherwin Williams. Its called WoodScapes. It is more of a stain than paint, but comes in all colors. You should and must apply the stuff with a sprayer. It will cover existing paint just fine as long as it is in good shape.
But to answer your question, there is not much you can do with old cedar shakes.