Just as with any automation. Put the track in Automation Write Mode and click on the Bypass Effect button (either in the MixConsole or the Plug-in window.
You can also select an automation track in the Project Window. You do this by hovering the mouse pointer over the lower left corner of the colored art of the Track Header. You’ll see a small arrow named “Show/Hide Automation” (if you have Tool Tips turned on).
Open the menu. beside the R and W buttons. If you don’t see the Automation Parameter for turning your plug-in on and off (bypassing), select “More…”. The “Add Parameter” box will then open. Click on the arrow beside the “Ins.” folder. Now you’ll se a folder with the name of your plug-in. Click on the arrow beside it. Now you see all the automatizeable parameters for the plug-in. Select “Bypass”.
Now you can edit the automation curve with the Pen tool, in the Arranger Window. One little annoying thing is that depending on your background color and the color of your track, the curve can be hard to see. Unfortunately, the curves takes on the color of the track. This can easily be changed though. Just change the color of the Automation Lane (not the main Audio Track) to a color with better visibility. Let’s hope that Steinberg sees fit to provide us with a “Default Color for Automation Curves” preference settings, in a future update.
Hope this solves your problem. Good luck.