I've seen that coop - they sell them here in Winnipeg at a chain of farm stores called Peavey Mart. For a pre-fab, it's REALLY nice.
If I recall, there is the small 'chicken door' on the far end......I would attach my run onto the end of the coop, and build it out from there.
I don't know if you can see in my avatar, but I built our run out of 2x2's, in 4x8 sections, and just screwed them right onto the coop. the sections are all covered in hardware cloth, which I also wrapped around the bottom of the coop itself, where it's raised off the ground, keeping the underside of the coop, and the whole run contained. I put a small door in the run, to let us in and out to be able to open the 'chicken door'. It's only 4-feet high in there, but not the end of the world. All in all, cheap to build, and seems to be working like a charm. I don't have a roof on mine, though....the girls won't go out when it's cold anyway.
What I WOULD recommend with that particular coop, though, is to place it up higher on some posts, or blocks, or something. Our girls love to hang out under the coop.....I've got about 2-feet of space under mine, but that one only has about a foot, if I recall. Just a thought.
I'd also line the floor with a piece of linoleum.......keeps things much cleaner.