I don’t use protools, but I assume it works in much the same way as other DAWs….
With the appropriate drivers installed on your computer, I guess you’ll then choose your SQ as the input device (and probably output too) from the protools preferences, then for each channel you want to record, you’ll be able to choose which SQ output it needs to be. Once done, probably best saved as a project template, as it can be a time consuming task!
In your SQ, you can assign just about anything to the USB outputs up (to a total of 32) in the routing section, inputs, groups, mixes, effects returns etc – check that you’re routing them to the USB B outputs.