I run a CQ18T, and although I haven't yet used ST3 live (still getting sets/songs etc. together) I did test it with my CQ, and it's pretty easy.
USB out of the iPad into the CQ, once that's connected, the CQ is a class compliant audio interface, so inside the ST3 app, you can choose which channels on the CQ you want to output your tracks to. Personally, I run multitrack versions of songs, with a separate click, cues, and various instrument tracks, which I anticipate muting or changing depending on the gig/band in the future.
Ive been using 4 of the CQs channels for this: stereo instrument/tracks all routed to the same channel (even though they are different tracks in the ST3 app), click, and cues routed to two separate mono channels (singer doesn't like as much click in her ears as the rhythm section, so I'll be running those separately.) Click and dues obviously only routed to IEM channels, not the mains.
Worked great in my test!