Using my title plugboard, I end up with "Book Title (#subseries, Book #) (Star Wars, Book #)". In the library GUI the Series column keeps them all in order according to "series:Star Wars" which is where in the overall canon order the book goes. Although I admit I haven't actually gotten around to sorting the order out yet.
Similarly,
Code:
title: Magician's End
Series: Riftwar [27]
#subseries: ChaosWar Saga [3]
For listing in order, go with main series/universe order. Then list #subseries (
custom column, type "Text column for keeping series-like information") afterward, where it won't interfere with the sort order.