easiest thing to do is use MDLOps' (
http://www.starwarsknights.com/tools.php#skmo) "renamer" function. There's a tutorial in the readme that shows you how to do it :)
but yes, to answer your question.. the info for telling the saber what color to use is contained in the .mdl file. Hex editing can change the color, but MDLOps is much easier...
Renamer usage:
1) start mdlops
2) click 'select file'
3) browse to directory that has your .MDL file.
Select the .MDL and click 'open'
4) click on 'read model'
5) click on 'renamer'
6) type in a new texture name in the "New name" box
7) click on the mesh that needs its texture renamed
8) click "change name"
9) when you are done changing names, click "write model"
The model will be written to the same directory as
the original with the name model-rbin.mdl and
model-rbin.mdx