I’ve only been using motion for a couple of weeks, but have found the following useful.
select a layer or layers in the project pane right click, and select solo, this will hide the other layers when playing the project and allow you to focus on the ones you want.
You can also deselect the tick box next to the layer in the project pane to temporally remove it from the project.
If you need to clean up the project pane using the disclosure triangle to collapse groups is handy.
Hope this helps.
Paul
same same but different.