Hi,
The HX effects integrates with existing stomp boxes very easily. It is limited with only 2 loops but you can get really creative. I did that for quite a while and here's how I had everything set up. The time based effects that I owned and always kept in my amps FX loop were plugged into the physical cable chain heading to and from my amps FX loop. They were all MIDI capable so I used MIDI CC and PC messages sent by the HX in Snapshots to change parameters etc per patch. I kept my 3 drives, fuzz, and compressor in front of the HX just like they were going in front of an amp. The few odd pedals that I wasn't always sure where I wanted them were chained together and placed in the HX's other send/receive loop so I could put them anywhere, even route them into my amps FX loop if I wanted to.
If you want to get REAL creative, you can always get a MIDI capable loop switcher like a Boss ES5 or ES8 and place them into the HX loop and use MIDI to control it all.
Bottom line is there are always options. Just be aware when you are using either of the HX loops you need to be mindful of the levels and make sure all your ins/outs are set accordingly for Inst or Line.
Best of luck!