I think it might be possible to have up to four layers ‘working’ in SE sound and controller-wise, but they just don’t ‘show up’ under the Sonic SE Edit Tab to the user unless you build some custom Macro pages and Scripts.
I could be wrong, but I did notice some of the HALion factory presets I was able to load in HSSE seem to have more than one layer, and also have a complete macro page for each layer:
Later, I tried to make some of my own multi-layered presets in Halion 6, which I then ‘Exported as SE Layer’. Since I had no macro pages in them at all, I just got a blank Edit Tab in Sonic SE; however, all of the layers still ‘sounded’ as expected, and I could access the Quick Controls for the ‘top most layer’.
Next, I tried some things like making a layered preset for Sonic SE with H6 from “Factory Content” that included macro pages. I’ve not yet been able to create an SE Layer that will display both macro pages (nor both sets of Quick Controls) in SE so far; however, I can nest layers in a way where ‘one’ of the Macro editors shows up in SE, while all of the layers play/make sound.
All of this leads me to conclude that if you want multiple layers in SE, with a macro page for each layer (Like we can get with Sonic 3), then you’ll need to do it via some sort of custom Macro/Scripting options.
Another way to simulate the effect of multiple ‘layers’ is to export each individual layer from Halion 6, then from inside SE itself, make ‘Multi-Presets’, where your layers are simply in different Slots in the SE Instrument Rack. Just have them set to the ‘same MIDI channel’ via the MIDI Tab.