Unfortunately it seems as if people don't check the skinning section all that often. Still, when they do, they tend to be rather helpful.
Here's a couple tutorials from Jedi Outcast:
Skinning for JA isn't a whole lot different. I think there's a slight difference in the sound setup, which is why you can use JO skins in JA, but the sounds don't always work.
Try searching on various sites for Raven's skinning tools. It's exactly like their JO tools, but they include a small paragraph on the differences between JO and JA skinning.
Keep in mind not to crank up the compression of your image or sound files, otherwise they either won't show up, or worse they'll crash the game on you.