Morphology likely wasn’t working because you didn’t have the .tri files to go along with the character body meshes and outfits. They often come packaged with Bodyslide compatible armors, but occasionally you’ll need to rebuild armors with Bodyslide. I made a guide of all this here.
As for SE/AE compatibility, the only incompatibility would likely to be caused by different slider sets. The mods are built around LE CBBE/UUNP sliders, whereas SE nowadays often uses BHUNP/3BA CBBE. I’m working on making those new sliders compatible, though.