As with any signal-chain related stuff, you have to think about what works best, especially when dealing with pedals that may have certain requirements (gain staging, dynamics, etc.). At one point (in a simpler time) I ran most of my things in the loop except for one or two in front. Now I have a signal chain that follows conventional wisdom but allows for me to do some moving about of where things are. While I use a loop/switch unit that has programmable patches, not everything needs to be in that system. some is out front and some behind...and having MIDI implementation means you don't have to have those pedals looped, unless you're playing with chain order or parallel effects.
Cool, you're basically getting much of the advantages of a loop switcher on a manual level by having those two mixers. Here's my setup (I've done my best to show the order of the audio chain (orange, numbered), the loops (green numbered) and the MIDI (blue, numbered).
You can see that things like the compressors,Spark (clean/colored boost), Synths (FI & Mantic) are out front of the loops, then the delay/verb are after the loops. The MIDI Implementation means that the FI, delay & verb are all effectively in their own loops, just not movable in the signal chain.
In the past, I've also had chorus and delay & verb in my crossover loop. but since those pedals can be HP's individually I don't need them there now.