I'm not quite sure what you think you would gain stage?...So there is no actual input gain staging ...that is now confusing me more...
In any case I now have all my levels within visually decent levels without pasting the red on the outputs and hitting the orange pretty steady on the input, still can't make a red happen on the input led's though ...but the sound is glorious ...so I a can live with the confusion.
In a traditional guitar rig, what would you do? This is what the Axe Fx models.
The Instrument Level setting (not Input Trim, which is a setting within the Amp block - I think Cliff had a brain fart in his post ) is for optimizing the Analog to Digital converters for signal to noise. It does not affect the input gain (volume) or the tone.
You would typically increase gain before the amp with Drive or boost pedals, or EQs, etc. No different here...
You can then increase the gain in various ways in pretty much every block.