there are a ton of possibilities. The most native one is to create a blend map:


white is 100% and black is opaque. You can add selections or random filters to this blend map (be sure to only paint onto the blendmap! open channels and deselect everything but the blend map then paint onto it)

the biggest benefit of working with layers and maps is to be able to exchange and redo or change things with a few clicks.


Models, Textures and Levels at:
http://www.blattsalat.com/
portfolio:
http://showcase.blattsalat.com/