When running the plexi setting unboosted, I usually go with the high gain input and bump up the gain, bass, treble and presence. In this case I wanted a tone that I could play with all afternoon without destroying my ears, then occasionally hit the Henning boost to bring back the treble, bass, gain, and tighten it up in a way that I can't do without a boost.
Another thing I like to do, is set up the plexi setting for no boost, then boost it with the Bion. But my favorite way to run the Penta is to hammer the clean channel with a Line 6 Uber Metal set to Pulverize: