What trench cover did you get?
To the OP, I've got 2 black lab mixes. I took my rear seat out, and put a Weathertech liner meant for a 4 door in.
I leave the liner in all the time, and when the dogs are going to be riding in the back I just toss a blanket back there, more to catch the hair than anything else. At first I loaded them in through the rear gate, but for my last trip I had a hitch mount rack on, so I tried letting them get in on the passenger side and they just hopped right in. I'm now re-thinking my plan for netting to keep them in with the roof off; I was planning on setting it up with cargo on one side and dogs on the other, now I'm considering cargo in the back, dogs in the "middle" (that way I can get at the cargo by opening the rear.)