G'day Katoa
Are you wanting to do some side trips along the way? There are some good camp sites in Litchfield NP, such as Buley Rockhole. Robin Falls is a bit south of Litchfield NP - only done a day visit, and the sites seem ok, but not brilliant - they are right along the road that goes in to the falls.
A bit further south again is the Douglas Daly Tourist Park - I'd recommend that over the camp site right at the Douglas Hot Springs, which is a bit exposed with not much shade and pretty dusty. The Tourist Park is great, and only 10 minutes to the hot springs. It's probably about 2 hours south of Darwin, and will be the first place we go to to test out our new Aussie Swag
At the bottom end of Kakadu NP are a few good spots - Gunlom and Koolpin Gorge being the top two. But they're both a good hour + off the highway, so definitely not worth it if your aim is to head south as quickly as possible.
Next stop - Katherine. If you must stay in Katherine, I'd go for either Springvale Homestead, a bit out of town, or Knotts Crossing in town, but the preference would be Edith Falls in Nitmiluk NP well before Katherine or at Katherine Gorge itself.
Can't comment on Mataranka as I haven't been there, but definitely can comment on the Devil's Marbles near Tennant Creek - that's a must see!
There are plenty of rest stops along the side of the highway, none too flash, but they do the job. Can't really comment much further south as we've basically done 8-12 hours a day to get out of the territory, the Kulgera Roadhouse has some good facilities though, but is a bit exposed and trucks come in and out at all hours.
Hope that helps. Don't forget to book if at all possible!