Thanks for posting this. I battle the same problem. I will be curious what others have to say.
I've been using the Helix at home and for gigs since about the time it came out. Here are some things I do that seem to help.
1) Minimize the number of presets you use. Typically I stick to the same preset for a majority of songs, and only use others if I need to nail the tone on a specific song.
2) Use a Decibel Meter app to balance volume between pedals and presets. I do this at home where I run my Helix through an acoustic amp (set flat). This gets me pretty close, but I've noticed even when it's perfect at home, it's not so perfect live.
3) Don't be afraid to make a quick adjustment in rehearsal (hopefully closer to live configuration) or live and save it.
The biggest problem I still have is the volume difference between an amp's clean setting and one with a OD pedal. I will be watching to see what others have to say.
