jimbo1001,
(I’m assuming you are using 3.5 R3.)
There’s currently a known issue where if you apply a texture map to a subtool it will always take on the currently selected material, even when a material has been embedded into the mesh. There is a workaround to embed the material in the texture map - see Svengali’s post here:
http://www.zbrushcentral.com/showthread.php?t=78792
Otherwise the simplest way is to convert any texture maps to polypaint, and embed the material of your choice into the mesh - if you do this after polypainting then be sure to just have the Draw:M [material] button active so you don’t wipe your polypaint. The SubTool Master plugin makes embedding materials in subtools easy.
HTH,
Marcus