Attention all other noobs:
I've figured it out so I'm going to tell you about it. No one seems to want to answer this type of question or lend any assistance in this area of BF2. Strange isn't it? Here's what you got to do:
1) After downloading BF2 ModTools, read the getting started and Jedi side creation documentation.
2) Pay close attention to the Jedi "side" creation documentation.
3) Set up your side according to what the Jedi side creation documentation tells you to do.
4) You will start by putting your side folder in data_XXX\Sides\(Your side's folder name) CIS is an example. Then there's the five files that go in it. You can find these in the ModTools\Assets\Sides folder.
5) Now goto _BUILD\Sides and create a blank folder for your side in there.
6) Now just run the Modtools VisualMunge from inside your mod's _BUILD folder. That's all. Make sure you created a world first, obviously.
7) Go find your side in the BF2 Addon\XXX\Data\_LVL_PC\Sides directory.
Pay very close attention to every step you take here. But, do the example set up in the tutorial's Jedi creation folder first. Also, check your side's *.lvl file size before your try to use it. CIS is 98K. If you have any questions, drop me a line.