PAK files don't need to repacked after you have extracted the files with the PAK program from Vercingetorix. R:TW first looks at the PAK files but if they are not there it will look for them inside the normal directory structure.
If you extracted the files then the tool makes something like:
You then copy the UI/etc and paste it into
\Rome - Total War\data
If you extracted all packs then do this for all created directories and you can then rename/move the PAK files. If you only extracted 1 PAK then only rename/move that particular PAK file.