I just got my sq5 today update it to 1.3.2 and start to program the scene for difference artist I work with, I found that when save and changing between each scene the stereo input and output setting stuck to the previous scene setting it not changing to the current scene recalled
The stereo configuration ist global for all scenes of a show. This was discussed several times here in the forum and you can find it also in the reference manual.
So, you can define some stereo inputs at the end of the input list and assign your inputss to that on scene basis. This together with the frely definable layers would lead you to the desired result.