I’m sure these questions have been answered by now, but here are my contributions:
Obviously using a midi pedal for the pickup machines (can you recommend one?).
I use a KMI Softstep 2 pedal, with KMI expander for the MIDI DIN connection.
Then going from a mic’d amp into the OT? Or using a preamp? Using the cue outs for other pedals, and back into the OT?
I still play guitar, but after taking up viola/electric violin and getting more serious about those; as well as incorporating synths/samplers, I stopped using real guitar amps. I now use a full range powered speaker as my “amp”. A decent tube guitar amp with the power tubes (not just the preamp tubes) cranked is a wondrous sound indeed, but since I no longer specialize as a guitarist, it’s not worth the trouble for me.
A decent mixer with at least one aux send bus gives you a lot of options for routing audio in and out of your OT. Which way is the “right way” depends on how you like the results of each approach. Currently, I plug electric violin/acoustic viola pickup into one of the mic/preamp inputs of my mixers. The preamp boosts the pickup signal level to line level. The OT (at least MkI, which I have) seems to work best with line level (0 dB) signal - I don’t like the results with typical guitar level (-10 dB) signal going into OT inputs. I have in the past used a Fryette SAS tube-driven pedal as a preamp, probably my favorite overdrive pedal. It doesn’t have guitar cab simulation but nevertheless has a full-bodied overdrive that I love with both guitar and electric violin, and it sounds great as clean preamp for acoustic viola, with the gain turned down.
The aux send output of the mixer goes into Input A of the OT. The OT main outputs go into two mic/preamp inputs on the mixer, instead of the aux returns or the line inputs. The reason is I find the output level of the OT MkI to be a bit on the quiet side - I like how it sounds in the mixer with the preamps. I don’t know if this was changed on the MkII but on the MkI, the Volume knob only affects the volume on the headphone out - you have to pull up a menu and adjust the gain to affect the Main Out level - so much easier to just use preamp gain knobs on the mixer to handle this, during the stress of a live gig.
It is certainly possible to route the Cue Outs to other gear, then route the output of that gear back into the OT. I’ve thought about doing that with the Eventide H9 or my Cocolase. Instead I am saving up for a new mixer that will give me more than 1 aux send. Then I can put the OT, H9, etc. each on their own aux busses - giving me a lot more control over the signal levels of each unit in the mix.