I downloaded a clone assassin skin and copied the common and rep folder into the side folder. I put all the clone assassin files into where they go, but now I'm having trouble editing the rep.req and the lua files. Could some give my a short tutorial on how to do it.

Read the BF2 Jedi Creation.doc. It tells you how to make .req files and what to do with them. Might I suggest even reading all the documentation. That's what it's there for anyways.

Too edit a .req and lua, drag and drop either file into a notepad of your choice.