In Zbrush2, I made a quick recorded script of how to properly embed different Shading and/or Materials, into a single Texture map using Projection Master. You can find the original link here: http://zbrushcentral.com/zbc/showthread.php?t=18153
For Zbrush3, I re-visited it, and made a tutorial out of it.
By default, using Projection Master, creates self-shading, which will damage your existing textures. You can avoid this by making your canvas a Flat material first, before painting.
The Tutorial will do the following 3 things, and it will use a technique, used by the FlatCanvas plug-in I created.
1st it drops a fiber filled ring, using shaded option.
2nd it drops a shiny ball, using material option
3rd it drops another fiber ring, this time with both shaded and materials on.
[Download Tutorial Script Here](http://www.mediabakers.com/files/PM_Options_Tutorial.zip)
[FlatCanvas plug-in](http://www.mediabakers.com/files/FlatCanvas.zip)
original FlatCanvas thread
PS. For those new to Zbrush, and don't know how to run a Zscript Tutorial, here's how.
Goto the Zscript palette, and press Load, and pick my zscript txt file.
At the bottom of the ZBrush3 UI, is a pair of arrows, letting you know you can drag it up.
Drag it up to expose the script GUI area, and press the Play Button.