I may have found a solution (have not tried it yet but should work, only got the pedal 2 days ago).
Set up a preset that will use both Path A and Path B.
In Path A, set up the bass side of the instrument using what you might normally use (for me, usually a Phase 90, Send/Return from an external Sans Amp)
In Path B, set up a volume block set to 0 (to mute the input signal), followed by a second Send/Return block and whatever effects chain you want for the treble side.
When plugging in the instrument, plug the bass side into the left input and the treble side into Return 1/2--and make sure the return you use is the one you assigned to the Path B block.
While I know this is not a common setup for most, one of the main reasons I bought the HX Effects in the first place was to give myself the ability to fully utilize any split output instrument I have (I have a Chapman Stick and a specially modified Squire VI in which the 2 lower strings go through a bass output, and the top four through the treble, with the ability to send all 6 strings together).
If anyone has any other suggestions, I am definitely all ears!