Am I correct in thinking that if you tweak a material you cannot use it in a 'material template' unless you save it to the library first?
If you have it in the materials list used in the scene you can reuse it for other parts. The material will be available the next time you open the BIP or KSP file, but otherwise will not be available in the Library until you save it there or to another location of your choice, but you would need to add the path to your custom materials for the library database to locate it/them.
Martin