Hmmm, after talking with the guy who set the server up, it turns out that we do have the ability to use modded jars, despite not having all the fancy server controls. So here is what I did. With Filezilla I deleted everything on the server (except white-list, ops etc). Then using the multicraft client I allowed it to set up a 'default' server. DL and extract FTB modpack, in the modpack folder change name of the FTB Beta A.jar to minecraft_server.jar. Once again using Filezilla I copied the 4 folders in the modpack folder onto the main server directory. Then I opened the jar folder on the server and replaced the jar in their with the one I renamed in the modpack. Delete the world folder if you want a fresh world with modded world gen.
That should be it. The weird thing is is that the multicraft control shows the server as offline, despite being able to log on and play.
I think I might try and convince the guy to change providers before RP2 comes out and we take FTB seriously. I dont really trust multicraft.