You will get a lot of differing opinions on this one. Do you want a permanent rack or something that can be removed? There are a ton of options out there depending on your budget. If you only plan on hauling a 60lb kayak then personally I would install some Thule or yakima rails into the top.
I use a similar setup to the Thule and Yakima tracks with load bars, although mine is Rhino-rack. I don't use kayak carriers for my low-end sit on tops...just ratchet straps. For a factor of safety, I also run a rope through the bow eyes and down just in front of the mirrors to the rock rails.
When I first got my Jeep last summer and didn't have a roof rack for it yet, I was able to just strap my kayak right on top of the roof. I have a flat-bottomed boat, so that made it really easy...just threw a few towels underneath and strapped it down tight. Now, I have a Yakima roof rack that clips in under the roof where the doors close. It's removable and I only install it when I'm taking my kayak or surfboard out. Of course, if it's a nice day, you can just take the entire top off and strap the boat to the Jeep cross bars. That's my plan for Sunday.
Keep in mind that using ratchet straps will allow you to overtighten the strap and it could deform/damage your kayak. Use cam buckle straps to prevent this. I looked all over the web for some good cheap cam buckles but ended up finding the best deal at walmart of all places. $20 bucks for 2 cam buckle straps, 2 bow/stern ropes and some foam V pads for carrying on top of a car. All I'm using is the cam buckles but it still came out cheaper than anything I could find online with shipping added in.
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