Creating presets using Stomp's send as output worked! Thanks so much for that tip. Is there a difference here between having a Send L block in path A vs. dragging everything down to path B? Either way I get a slight bleeding still in path A (I still get a little bit of sound through main L/R when I thought I sent it all to send).
Other that that, I figured out all the connections! This really is an incredible piece of technology. I forgot that my ABY box also has a tuner out, so I just hooked that up to Rocksmith. A to my amp, B to the Stomp, Tuner to my computer Rocksmith cable. On the Helix Main L/R are to speaker monitors, my amp send goes into aux in (had to change this in the global settings), and Send is to my amp return. Like I said, except for that bleed in the A path it's working.
I should also note that actually, this solved a ground loop issue I had. My rig is waaaaay more quiet now, so much so that I keep checking if the noise gate is on accidentally.