Edg3k

Hey guys. Sorry if someones mentioned this before, but Im not sure what to search as I'm pretty new to the whole thing. Im trying to find a way to add certain mods to my Tekkit Kerplunc server. So far Ive managed to add a few via the FTP but only into the plugin folder, some I have say the NEED to go into the minecraft.jar which, I have no access to, and then some say they need to go into the mod folder to, but when I put them in there and update the server they seem to get wiped out from inside it. Ive looked around but I cant find anything clear about doing so. If anyone could gimme an idea of what I'm doing wrong (probably everything) I'd much appreciate it.