After the transparency map is finished you can paint the color map (a good idea is to keep the transparency map in the alpha channel of the diffuse texture for the hair).
You can paint over the transparency map, overlay textures of real hair or anything else (dirt, rust textures) to give more variations to the diffuse. Keep in mind to start with a flat color for the entire texture and add details on top; you should avoid the first approach in the picture bellow and go with the second one... keep the color around the edges of the hair the same as the hair color... otherwise it will look bad.
Back to menu.
3.3. Hair geometry
Once the textures are finished go back to the 3d application and start modeling the geo for the hair.
Pay attention to the outline of the hairstyle, the silhouette.
Start with simple geometry and block in the main shape of the hair... you will add more tessellations later if it will be necessary but for start keep it simple. When creating the geometry for the hair I usually start with a clump of hair and then duplicate it and move it around... I repeat the process several times until I will cover the entire head then start tweaking the geometry to better suit the hairstyle I want.
For volume hairstyles try not to model the geometry for the hair like in the picture below because it will require a lot more planes.
Instead aim for something like the next image where the planes with alpha are almost perpendicular to the head surface so that they will add a lot of volume to the hair. Now with some patience you will end repeating the process over and over again duplicating this clump of hair and moving it around to populate the hair. Spend some time moving and scaling the planes with alpha, move vertices around or the UV's if stretching in the texture will occur; give as much variation as you can, with one clump of hair you can make some neat hairstyles.
You can use this method for dreadlock 1 and chaotic hairstyles (Varga's hair was done in a similar manner... there is a chapter at the end of this tutorial showing Varga's hairdo and textures).
When tweaking I use the following trick: Maya has a lighting option for using all the lights in the scene in rendering the view port (keyboard shortcut 7) if you do not have any light in the scene then all the geometry will render black but still have the transparency working; be sure to have a light background (for other 3d apps I am sure there is something similar or you can create a material with color and diffuse black but still displaying the transparency map).With this option active you will pay attention only at the outline of the hair... keep moving around the hair and adjusting the vertices until you are satisfied, track, dolly, zoom and move around the head to see it from all sides.