You can use many plain ole lumber racks or ladder racks as they are called. I found the Thule XPorter rack system recently, and it looks to be very high quality. My suggestion, get it up out of you bed space and use that room for other stuff. Compare weights of kayaks carefully. I own five, going back 20 years. You go to Dicks and get a $259 yak, that's one thing. An easy mistake to make, unless you are a very infrequent casual paddler.
Find a real paddle shop and look at Wilderness Systems Pungo, new or used. Great boats and two of ours are 12 footers weighing about 50 lbs. this will matter if your loading up high. The smaller you are, the more so. I will caution you against buying a cheap (often heavy) yak. A double worse version of this played out a thousand time story is buying a cheap/heavy shorter kayak, to save money or reduce weight over the long cheap heavy yak.
A 10-12' or longer yak up to 14' will track considerably better, be faster, more efficient, and have ample room for your comfort and a fishing rod or three, soft sided beverage cooling system, portable water proof classic rock machine, or whatever. They last forever if cared for, avoid warping from improper storage in sun, and wipe down twice yearly with liberal application of Aerospace 303. Get a good boat. That's my advice.
Ally pack canoe....
If space is really an issue, and money not so much, check out the Ally Pack Canoe. 16.5' DR (downriver) model. Now sold at REI to my surprise. I've had one ten years and floated numerous remote rivers in Alaska with it, mainly above arctic circle, hundreds of miles from nearest town/village, 80-120 miles each trip. My buddy bought one too, for same reason. Holds about 800 lbs, I'm 6'6" 320 lbs and carry wife, two weeks of food, gear, guns, fly fishing gear, tent, stove, fuel, etc.
I've tested personally, and is great in class I-II rivers easily. Great on ponds and lakes of course. Aquabond will custom make two piece canoe paddles. Canoe breaks down and stores in large backpack. Skin is made of incredibly durable Tarpulon, a lighter version of Hypalon used on Zodiac rafts. Ally is original pack canoe, made in Norway, and used in expeditions all over the world since the 70's. It's the bees knees man. Love it.
Ally pack canoe on REIBergans of NorwayDan