please be more specific.
how many files can you have? it depends on the MOD, but, if you mean models and sound files, just put them in the corect folders in the correct MOD folder. When people try to download the .BSP, those sounds and models automatically go with it. if you want to put it in the Map vault here, jut include them with it and tell people to put them in the right spot in the map description. Or, just use a .BSP with no new stuff.