I run my Helix through my tube amps often and I am very happy with the tones I get. I rarely use the global EQ, so I would suggest turning it off and only using it for adjusting to the room you are performing in.
The Helix is at unity gain with the big volume knob all the way up. This is the first thing I would suggest you try. Also, be sure you have any cabinet and IR blocks bypassesd. You didn't mention if you are running in the front of the amp, in to an effects loop, or 4 cable method. This info could help with troubleshooting.