OK, I figured it out. Similar to the instructions in the manual, but you are right about the AUX level. Either a DI or a clean boost pedal will be needed for the AUX or MIC input.
Helix:
Input 1 Use Guitar
Input 2 Use AUX or MIC
Merge input 2 into 1 so both will be output into USB 1-2
Put whatever effects you need for both sides
Go to Menu then Global Settings and assign AUX or MIC to Re-AMP SRC 8, GUITAR was defaulted to Re-Amp SRC 7
DAW:
Create one stereo track,Inputs 1-2
Create the melody dry signal MONO track input 7
Create the bass dry signal MONO track input 8
All outputs should be 1-2
Plug the melody side in guitar and bass into AUX or MIC
Arm all and record. I got the effects of both sides in the stereo track, and separate clean signals in the bass and melody mono tracks
I did not try using the mic channel. The problem is they do not allow the returns to be selected for USB 7-8 which are the two Re-Amp inputs in USB.
You only get the choice of AUX,MIC, or GUITAR for 7-8 :(
I used headphones to monitor.