Hi Erik,
Every piston, key, stop etc can be mapped to 2 separate inputs. Sounds like you are re-using the "Primary Input" for the second piston, which would explain why the second piston wipes out the first one. Set the thumb piston on the Primary Input, then choose Input 2 for the corresponding toe stud.
To access this function, don't choose "Auto-detect" when you right-click on the piston - choose instead "Adjust MIDI/trigger settings manually...".
Check out Pages 152-153 of the Hauptwerk User Guide.
Andrew