Where are the .mat files stored?
Most likely the best thing to do is stoer them in a folder (Textures, just create a new folder for it.)
Put all your .mat files in there WITH the .dds , .tga... or what ever you are using.
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You can make sub folders, like
Snow_Textures
Rocky_Textures
IjustWantToShowYouHowThisWOrks_Textures
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Also, did you have your mods name (if isolated Full Conversion) into the Redist/Resources?
The Custom storys has to be in there too for loading your files.
->
<Directory Path="/custom_stories" AddSubDirs="true" />