Assuming a MIDI encoder is connected to the MIDI output port of the Rodgers.
The easiest way is to remap the pistons to not control the Rodgers combination action by resetting each piston you want to use strictly for Hauptwerk to "a zero state" - (no Rodgers stops being turned on by that piston). Do this by turning all Rodgers stops to off, pushing the Set button and then "assigning" that (no Rodgers stops activated condition) to a piston. So when that piston is pushed, it will not turn any Rodgers stops on. In other words, that piston should output MIDI no matter if Rodgers stops are being controlled or not. You can then use that piston to control only Hauptwerk stops.
Continue doing that procedure to as many pistons as you want to disable (from controlling Rodgers stops). You may want to leave some pistons still controlling Rodgers stops. You can also assign some pistons to control both Rodgers stops as well as Hauptwerk stops.
Rgds,
Ed