Use the two DSP lines in the Helix display as separate channels. On the far left of each line, set the input to be the 1/4” guitar input. At the far right end, set the output of the top line to be the left 1/4” output Jack and then set the output of the bottom line to be the send of loop 1. Plug your amp that will get all the effects into the left 1/4” output jack and the amp that will get the rotary into the send jack for loop 1.
On the top line, add all your effects (except the rotary). Add the rotary to the bottom line. Don’t add any amp or cab blocks if you are sending the Helix outputs to real amps.