It's really simple to setup and you can do this in Standalone, or with Pro Tools. You will need a mic plugged in to the Mic In of the Eleven Rack. Switch the Rig Input of the Eleven Rack to Mic - and you are set!
Now in Pro Tools, the input for the dry/mic sound will be Mic, and the input for the effected sound is Eleven Rig L/R. You can even record both of these inputs at the same time. You can also re-amp your dry track later on. There are so many options with the Eleven Rack, break out your acoustic and try this out for yourself.