Say you have a patch model with 200 patches and you want to use a 3D paint package to paint the fur color. Go ahead and load the surfaces into your paint package, paint color, and import them into Maya as your surface's color. This should create a switch node on the material's color to tell the material which surface gets which file texture. At this point, disconnect the switch node from the material's color, then connect the switch node's output attribute to the fur description node's base or tip color attributes... then bake them. As you can imagine, this method is not restricted to painting fur color...

Fur does not recognize file textures mapped to light color, or the 'illuminates by default' attribute of a light.

To comb your fur, paint fur Direction. But, before this will work, you must paint fur Inclination so that the fur hairs are not perfectly aligned with the surface normals...you can do quickly using Artisan's Flood button.