[Rick]

There are specific palette indices that do different things:

0 - Border Color (Default: Black)
1 - Belt Color (Default: Blue)
2 - Transparent (Default: Green)
3 - Shoes (Default: Dark Red)
4 - Sleeves (Default: Red)
5 - Skin (Default: Orange)
6 - Body (Default: White)

Any color after index 6 are not affected and are shown as is. The default bodies are only 16 colors, however, you can safely increase this to 256 colors. Basically, fill any transparent areas with index #2.