Disney now has the early online check in available, I think you can check in up to 24hrs in advance. They have your welcome packet and KTTW cards ready for you at the desk. (They also do this if you show up at midnight...)
The way it has worked for me in the past, although I haven't stayed there since '09, is if you do have a pop-up or tent and in a designated pet loop, your dog can stay with you for as long as you are at your site with the dog. They are not allowed to be left unattended in one.
Way back when, I'd pay the 5$ a night fee, plus the kennel fee. I'd drop her off at the kennels during the day when we went to the parks and brought her back to the site at night time to sleep with us. This was way back when Disney ran the kennels and it was about 12-15$ a day.
I think with a pop-up or tent, there's more chances of a dog chewing through the sides for escaping, and being much louder with the barking.
But as most things go at Disney, the rules are made by whoever you talk to... and every one has their own interpretation of that...