Hello Pat,
It is a 2 step process, first defining which stops are associated with each scoped piston (with the Scope button activated, then turning on the stops, then assigning stops to a scoped piston) then second setting the pistons just as you would normally set any piston (with the Setter activated). I think you are just not understanding the function of what scoped pistons are and how to use them.
When you refer to your Accomp pistons, do you mean the Paramount virtual Accomp pistons, or the physical pistons on your console?
If you have assigned your physical pistons to other virtual controls (such as the Paramount divisional Accomp pistons) then you cannot use them together with the scoped pistons, it isn't meant to work that way, otherwise they will be fighting over the stops and causing incorrect registrations. If so, you would first need to cancel those MIDI assignments (right click on the virtual pistons, choose Clear all MIDI triggers..., then you can assign them to the Scoped pistons as needed (right click on the Scoped piston, A1 for example and choose Auto-detect, and set up as usual).
Once complete you need to use the scoped buttons themselves on the large registration control panel, *not* any pistons included with the virtual organ display pages. If you don't want to view the control panel after setting everything up then assign your physical MIDI pistons to the scoped piston buttons (A1, A2 etc.) making sure that your physical pistons are *not* assigned to other virtual controls.
Again, the master generals and scoped pistons are completely independent from any virtual organ pistons and will not affect their registration. Scoped pistons are an *additional* registration tool only. You cannot change the function of the virtual organ's pistons themselves.I created a short screen capture video (Quicktime .MOV format) showing how to do a basic scoped piston set up. I didn't add any audio explaining each step since I figured it was self-evident and I am not set up at the moment to do voiceovers, hopefully this will get you going.
This basic example defines all Great stops to Scoped pistons A1-A5 then defines all Swell stops to Scoped pistons A6-A10. Then individual registrations are created for each of those pistons using the Setter piston.
It begins by showing that each piston is blank by clicking on A1-A10.
VIDEO