Probably need to start here;
http://en.wikibooks.org/wiki/Trainz/Basic_Reskinning_for_beginners
Of the basic files in a train car or loco;
whatever.pm or whatever.im - mesh files, this is the shape the textures are applied to. .pm is obsolete, use PM2IM to convert them if you're updating old stuff.
whatever.texture - this is a compiled file which contains whatever.texture.txt and whatever.tga. When you reskin something that has a whatever.texture file, you use images2TGA to decompile it, that creates the whatever.texture.txt and whatever.tga files, which you can then edit.
Best method is to delete the whatever.texture file after the whatever.texture.txt and whatever.tga files are created so PEV mesh viewer displays what you edited in the .tga file instead of showing the original .texture image. You no longer need the whatever.texture files after that, those are only used for built in content. Other thing to check, if you're using something like paint.net or gimp, check the Save As options to make sure you're saving UNCOMPRESSED tga files, compressed tga files won't work.