Well if you try it out and have a specific question, let me know. I have it set up. I didn't think it was too hard to use necessarily.
First you just have to use MalaTree.exe to create the tree structure.
There are two types of items in Mala Tree: Menus and Gamelists.
So for me, my tree looks something like this
MAIN MENU
- MAME menu
- All Games gamelist
- Favorites gamelist
- NES menu
- All Games gamelist
- Favorites gamelist
For each item in the tree, you need to specify a layout.
For each gamelist in the tree, you also need to specify what emulator it's using.
You can order the menus and gamelists to be in whatever order you want.
Once you've created your tree file, you have to go into Mala's settings and turn on the Tree option.
Thats about all I can tell you without having it in front of me, but like I said, if you were to try to set it up and had specific questions, I'd be happy to help.