I use a m9 in the loop just for delays, verbs and modulations. All my gain stuff is analog (pedals and amp channels).
I just added an M13 to my rig last night (got it off craigslist), and I am doing something similar to this. I use the HD500 and DT25; the M13 is in the HD500 effects loop, and the "pre" effects feeding to the HD500 guitar in are coming from analog pedals. Actually doing parallel signals, running two amp models then merging them mono before hitting the M13. Running the 1/4" through the analog gear, and also using the VDI from my JTV59. Still working out some issues, and have yet another learning curve with the M13, but the overall effects are quite familiar since I've been tweaking with the HD500 since 2010.
I may end up actually putting an outboard chorus pedal in the M13 effects loop before the delays and verbs, not sure yet.
I like the challenges of making analog and digital gear play well together. The DT25 does make the HD500 a lot more useable; the feel of the amp is there, it's not so 'virtual' amp model anymore; the tactile feel of turning knobs on the pedals is also crucial; while programming everything is important with this gear, to a certain extent, you have to approach it like a painter preparing his palette before beginning. Sketch out the forms, determine the colors, then premix certain tones and shades so they can be applied when the time is right.
The M13 is fantastic for that "on the fly" vibe, when you want control over specific effects and pedals on/off, rather than entire scene or patch changes. Especially since I am relegating to a "post" amp model portion, before the L6Link hits the Bogner power amp portion of the DT. I think I will end up building a variety of M13 scenes with pedals in specific locations, or at least following some sort of logic to where / why the sequence occurs (mods, then delays, then reverbs?) Might put a comp or drive pedal into a 'clean boost' type slot, right after the preamp. But most of that will happen before the amp model / preamp, with the analog gear and the FX/FS that I set up in the HD500, also in the pre slot.