Thankyou David I followed this advice. Using the gain blocks as you suggested to adjust the path volumes. Works well when I'm using electric guitar (mags) for the top path and Variax acoustic sounds for the bottom path. This is all I need for now.
Next challenge will be to somehow be able to switch between the magnetics and other variax modelled electric guitars within the same path so as to be able to use the same amp, cab, effects etc. I've only just started playing around with it, but my idea is to create custom models within Workbench that essentially just use the magnetic pickups (ie - Magnetic blend at full), and then select these in the Variax input block in Helix.