If you plug into the input of the amp, as you suspect, the amps preamp is in the signal path -- "stacked" as you put it.
If you don't want the amp's preamp part of the signal path, then just take the plug out of the amp's instrument "input" and plug it into the effects return. Of course this bypasses the Ampeg's preamp.
If you want the option of switching back and forth between these signal path scenarios you will have to either manually unplug/plug the cable at the amp's input and/or effects return, or use a separate switching matrix system. It depends on what all you want to accomplish, how you want it to function for you as the user, and the amount of detail and/or complexity you are willing to work with to meet your goals.