Easy man, coders sometimes forget that not everyone has their natural born h4x0ring skills.
I'll try to explain everything as best as I know, please feel free to correct me.
First you'll need a server.cfg with the OJP cvars and stuff in it, otherwise you won't know what's on and what's not. Add me on firstname.lastname@example.org
if you have msn and I'll send you mine if you don't know how to add all the stuff.
You can also start up an ojp server via create game then start adding the vars from ingame via the console by writing "seta (cvarnamehere) (value here)".
So if I wanted to add "OJP_allowbodydodge" and turn it on, I would write "seta OJP_allowbodydodge 1" in the console. If I remember correctly, it's very important that you write "Seta" and not "set", as "seta" saves it and "set" saves it only while the current game is active. But I'm no coder so you'll probably have to double check that with ensi or Ace (or Hockney).
Now this is the part I'm not familiar with because I don't know what they use to create the batches. I would guess MS DOS batch script (ah-durrrr) but I wouldn't know what you would have to write. I was thinking of just editing the runojpenhanced.bat but it seems that the JampDed app works differently than that..