I was trying to make Scy and Shadowyard play nice together and this is the result:
Spoiler
(http://i.imgur.com/RLVF5PO.png)
To make them spawn fleets I had to edit the Vanilla economy.json and starmap.json with all modded systems, then archive the modded version of these files. I tried both with one then with the two factions and I think the number of fleets double for each additional faction. Here the log from the campaign simulation (https://www.dropbox.com/s/l2ll60k0kmlgdp7/SS_campaignGeneration.log?dl=0)