Ahh, my favorite places to camp. Been doing it since I was a kid.
Three areas come to mind. A good base camp is Jacob's Lake about 45 minutes from the N. Rim (beautiful drive). The advantage to this is that you first are a few thousand feet above Kanab and the temps are very nice. You can hit the N. Rim, and then head to at least Bryce and Zion as day trips. But, if you do a Moab hit, you can get Canyonlands and Arches and then half way to Jacob's Lake and hit Capitol Reef and Bryce. Then stay at Jacob's lake Campground and hit the North Rim and Zion from there or even Bryce as a day trip. jacob's Lake is always about 20 to 25 degrees cooler than down below. Kanab actually has one of the largest no kill animal shelters in the world with a whole canyon. There was a TV show at one point based upon it. They took the bulk of the Katrina Animals.
In Moab, take the moonflower canyon drive as far as your vehicle will let you as it gets progressively more interesting. Lots of petroglyphs and you end up on that backside of the Canyonlands area. Another amazing campground south of Blanding is Devils Canyon. I was there as a kid and the trees were NOT nearly as big as they are now. It is a beautiful place and from the entrance of the campground, you can see to Shiprock and hundreds of miles and see the milky way. Awesome. There are some relatively unknown places to go down there including a Canyon called Montezuma Canyon with a lot of Anazazi ruins but it is not a park or anything.
If you can, go to Durango if it hasn't burned down. It is a wonderful basecamp for many areas and daytrips into New Mexico and up into the mountains and maybe do the train.
Too bad you only have two weeks. You can't do all of this in that period. Another place to hit Great Sand Dunes on the way back. It only takes a couple of hours. Spring is best as there is water going right through it. I suggest a large loop from North to South coming back from Durango.
Kind of a scattered post but Awesome areas of the country in a relatively compact area.