Your problem should be fixable with a little testing. The Helix is a great sounding device. Here are a few things to try:
1. Create a couple of basic patches for testing from scratch. Maybe a WhoWatt 100 for clean and a Brit Plexi Brt for crunch. Keep these very basic.
2. Turn Guitar PAD on. I do not have active pickups, but with PAD off, I generally get bad sounds. Definitely a good first step.
3. Make sure your LINE vs MIC output settings are correct. This depends on what you are running the helix into, but Mic level vs Line level can make a big difference.
4. Keep your master volume at 50% (12 o'clock position) for testing just to make sure you aren't sending too much signal to the receiving device/speaker.