Depending on what the VMT file says depends on where the models go. If the models are for GMOD, then it's possible that they're setup to go into the model folder for GMOD. As such, if you move 'em into a different folder, they won't work, unless you preserve the same folder names.
Edit: Argh, my bad, that stuff is defined in the QC file, not the VMT file: the VMT file is for textures. The QC, however, is embedded in the model itself.