Setting scene levels can be quite difficult. I plan on doing a video on my whole approach to these things, but it might be awhile before I get to it, so here is a summary.
In the end, your ears are king. VU and LUFS meters will get you in the ballpark, but you have to listen at gig level and preferably in a mix to make the final adjustments.
My intention is to build all my future presets around a few three-channel amps (the gain levels of the three channels are achieved using scene controller 1). Each amp has a corresponding cab block and I tie scene controller 1 to the cab block level and use that to set the levels of the three channels appropriately. If I were running all purpose presets, this would be enough.
But I run one preset per song, and each scene correspond to each part of the song. So I use a filter block after the cab block tied to scene controller 2 to set the levels of each scene to fit in the mix and fit the song. For a lead I might switch to the y-state of the filter block to give me a slight mid boost.
To actually set the scene levels, I bought a Boss FS-6 and set it up to go +/- 1 dB on the main output scene level slider. This allows me to play with the band, and change my scene levels in 1 dB increments. When rehearsal is finished, I will go through my presets, and all adjustments I made to the scene main slider will be moved to the filter block.