Do you need to control the universes?
Make your tree as 3 strings 100 pixels 2 strands per string and drop it on your controller in the visualizer. It will distribute the 3 strings across three ports. If you do this for your whole display, xLights will "take care of it".
If you want to do it yourself, then you need to setup "Use start channel" on the model for controller, check Indiv Start Chans. Once the strings are shown, click the drop down on the right and you can select a bunch of options.
If all this is confusing, the zoom room will fix you up in a few minutes once they get to you.