I Run in to 2 Bose systems (L1 II with b1 bass unit and Tonematch) occasionally with a band I play in but I bypass the Tonematch using it only for vocals and plug into the analog quarter inch aux input on the base(it has its own trim control). In stereo with both poles, it sounds amazing. I ran an HD500X before and now my Helix using this setup. Are you running mono into the Tonematch or sending left and right into it? I once ran the stereo lef/right out of my Line 6 pedal into 2 channels on the Tonematch into one pole and got some nasty overtones. It wasn't good. The preset EQ's in Tonematch are great especially for OM-5 vocal mics which I prefer but I don't care for using them with Line 6 processors so I bypass the Tonematch. I'm assuming you are running Line out of your Helix.
Wallyg's post in Helix into Bose L1 Series 2 PA with Tone Match and B2 sub was marked as the answer