Good idea to set some kind of (inofficial) standard for this! I use input 1 for the guitar signal and input 2 for the bass part of an “A little Thunder” pickup (http://www.alittlethunder.com/).
What’s the current state of affairs regarding this in the stick community?
I prefer Input 1 melody, Input 2 bass. Seems more natural to me: on a grand staff the treble (melody) clef is on top, which also happens to be where Input 1 is on the pedal board interface screen layout.