The best way to compare levels is to use a RMS meter with A weighting. I use my Axe-Fx II as a sound card connected to my PC's USB and then use a DAW to record my presets and compare them. I like to record against a simple drum track, so I can hear my presets in a mix.
Also, make sure you aren't measuring or comparing your initial pick attack bc you want to measure the sustain. Lookup ADSR Envelope (Attack Decay Sustain Release)
Once I get all my sustain levels even, I make sure the pick attack doesn't peak the Axe-Fx II output. I try to leave 6dB to 10dB of headroom, so I have room for my Solo, Boost or Special FX Presets.
When listening to your presets in a mix, try adding a High Pass and Low Pass filter at the end of the layout grid. Remove as much low frequencies with the High Pass filter as you can, so you can get your presets louder bc low frequencies use a lot of level. Once you feel comfortable using the High Pass filter, try moving it to the left on the Layout grid to hear if it works better before or after certain Blocks but make sure you're listening in a mix and not just your guitar. I usually use mine right after the Cab Block and before FX or sometimes I have it at the end of the Layout Grid.