I am running stomp boxes in my effects loop. My method is convoluted, but has been working well for me.
1. Turn down the Global 2 EQ gain to -12db
2. Leave the Effects loop input at the default 0 db
3. Turn output 2 volume knob all the way to max on the front panel
4. Run amp block level at -22 to begin programming a patch and adjust as needed, while watching the meters in the Utility menu.
5. It helps that one of my outboard processors has input lights, so I can plug a guitar directly into it, view the input level, then plug it into the Axe FX output 2 and match that signal strength while feeding it with the Axe FX.
6. I have never tested the signal strength if I bypass the amp block and basically send my guitar straight through the grid and into the effects loop gear, which is what you want to do, but you can regulate the signal strength you are sending, in a preset, by turning down the input of the effects loop block.