I’ve got this setup and I’m not quite understanding your issue.
The yoke will have a button 1 and the throttle will have a button 1, but they are not the same control. If you assign autopilot to button 1 on the yoke, it isn’t also going to be assigned to button 1 on the throttle, unless you also assign it there, too.
The left and right box for each control, just allows you to set up two separate control assignments for the same function on that specific device.
I also want to point you to this, I’m hoping it will help you: