The Empire Tree doesn't move that much unless there are ships entering/leaving phase space (or loads of ships simultaneously disappear from detection). If you hold Alt while selecting one squadron, all other squadrons of the same type are selected (this also works for ships). Holding Shift at the same time will add ships/squadrons of another type to the units you have selected.

Theres a button near the top of the UI that stacks the empire tree icons to save space, that should help a bit.