I think all you would have to do is create the a sequence in side S2 with the correct number of channels, then inside xlights just map the channels to the correct network (make the SS's ether the first channels or the last channels). xlights should not be taking any of the network information out of the LOR files.
Matt will probably know more, I personally have not tested multiple networks yet, until mid september all I had was one 16 channel LOR controller, was waiting for my summer sale order. Now I have 80 channels of LOR, the ability to run 3 LOR networks, and a DMX network. Due to setting up Halloween, and working on Christmas I have not had time to do testing. But once the Christmas display is taken down I will be throughly testing every thing.
I do plan on adding SS's to my display for next year too, so I will let you know how I set it up.