OK, I should be a little more specific. Reinstall whatever flavor of FTB you are using (I'm using Mindcrack) - That's your /coremod, /mods and /config folders and all files within. In your root folder of the server you should have a /jar folder. That's where you'll place the jar from the MCPC+ zip. Rename it ( I named it ftbserver.jar). Reboot your server, and then you should be able to place plugins in your /plugins folder.
There is a problem with the creeperhost file repository and the MCPC+ jar always comes out as a 0byte file. That will do nothing if you do not replace it. But first you need all the relevant files that make MCPC+ into an FTB server.
What I did to accomplish this was install the flavor of FTB that I wanted to run (via panel) and then installed MCPC+ on top of that (again via panel). I did it this way as to not mess with any of the lower level crap that makes the web panel work just in case there was something I didn't understand like customized start scripts per install packages. Then I did the below
Grab your own copy of the MCPC+ server (from the MCPC+ wiki, github, or Jenkins) manually via server commands or good old uploading.
If you still want the CreeperHost buttons web panel crap to work(and probably other stuff, I've always renamed it)then rename it craftbukkit.jar.