While discussions on how to use OFP and/or servers aren't OFPEC material, and they are especially not OFPEC comments, here goes:
You set up the mod folders just like on your "play" computer". The server is then started with
an extra -mod= parameter, just like in windows.
Depending on if you run a windows-based OFP server or a linux one, the incantations are slightly different but still similar. Take a linux-based ofp server, for example. Lets say you have put ECP on it and some other mod folder, call it "wizzy" ;D
To start it, you'd do
./server -config=wizzyserver.cfg -mod="@ecp;wizzy"
With only one mod active, that would be
./server -config=wizzyserver.cfg -mod=wizzy
For further info, I'd suggest doing a search on the
official BIS forums since I believe that any minute now a moderator will come here and confirm that OFPEC is not the place for tech support questions. Right?
Good Luck, Wizzy!