@mxqn it took me a while to figure it out but what worked for me was to move all of the autopilot rotary knob functions into SPAD and make sure there were no duplicate binds in MSFS.
In addition to setting up binds for clockwise and counterclockwise for each of the 5 selections (ALT, VS, HDG, CRS, IAS) I also added event triggers for knob push for VS (button 20), HDG (button 19), CRS (button 18), and IAS (button 17) and that prevents the issue where using the rotary knob for anything other than altitude would still change the altitude along with say heading or vertical speed.
If I could attach a pic I would. I am glad I finally figured it out, was about to give up on SPAD and not buy a license but now that I understand it I plan to keep it - so maybe I can publish a profile or snippet next week.