first set up mala, emus, layouts and gamelists normally before making a tree.
Open Malatree and you will have a menu like shown below (make sure Malatree is in your
mala folder.
On the right under Top Node this is the first screen to appear when using the tree, you can name this what you like and pick your layout to use from the drop down box
Now click on add menu, you will now see a + sign next to your main menu on the left, click the plus and it will have new node, click on new node, these nodes are your emus that will show under the main menu. now on the right name your new node, say 1st one is mame now pick the layout you wish to use when going to the next screen which will be where you choose which gamelist to launch.
Now click add gamelist and another + sign will appear which will be a new node, click on new node now on the right name this what you want for the gamelist like All Games, Cocktail etc then choose your final layout, this will be the layout where your games will show up.
Then choose the emulator for this node and then choose the gamelist eg: All Games.mlg
Now click back on the top node the one right at the top on the left and click add menu and repeat all of the above for your other emus. as I said at the start make sure all your emus and gamelists are already setup otherwise they wont appear in the dropdowns in malatree
You can use a snapshot on each branch of the tree eg: N64 console on N64 branch etc these need to go in a folder which can be chosen under gui in mala options they need to be named like so, say you menu structure is top node=Mala menu and you mame emu is called mame the the snap to show on the mame branch needs to be named
Mala menu_mame.png
hope this helps