I had issues at first too; just got my MC6 last week. And the weird dark background in the forums is a new development, it used to be legible.
I also find that in both the desktop editor and the web editor, the name of the MC6 won’t show up. But I watched the Morningstar video on the HX Stomp (on the front page of the Morningstar MC6 product page) and was able to get the Mod Duo to respond. Here’s what I did (note this is with the desktop editor, but it should work with the web editor).
Connect both the Mod Duo and the MC6 to your Mac via USB. Connect them to each other with a 5-pin MIDI cable. Enter edit mode on the MC6 by hitting D+F together. As long as the “Device” button on your Mac turns blue, you’re good, even if it doesn’t show the device name.
Press the switch on the MC6 you want to program and it should show up in the editor. Program it per the video (I won’t go into all that process here since it would be repetitive, except to say that I used CC #11 like they do in the vid and it works). Save your presets and exit edit mode.
Then go to the effect you want to control in the Mod Duo editor, choose the actuator drop down and select Midi Learn. Press the button you’ve just programmed on the MC6 and save your pedalboard. You should be good to go!