We've used the Thule "The Stacker 830" racks for about 6 years now. This is probably the simplest system available but requires a bit of effort for loading. These racks would require cross rails on your PUP/AF already.
Primary choice factor for us was flexibility; we only need the one set of racks for our two Ocean Kayak Frenzy models, and we could easily add a third on the car roof, and a fourth on the PUP roof if we ever wanted to (weight limit not withstanding) with a second set of straps. The included straps are plenty large enough to secure two kayaks however.
Installation/Setup is easy, but be sure the fasteners are snugged down tight. Recheck after a day in the hot sun as the bolts seem to loosen a bit as they expand in the heat. I have had the racks shift a couple times on the cross rails in strong cross winds (large transport passing), but the straps and ropes keep everything safely secured.
I also use a long cable lock system to keep the kayaks from paddling off on their own.
You can see the setup on the TV roof here, probably had bikes on the pup roof at the time. Can't find a pic with them on the pup roof, but that is where they usually are.
Kayak rack on a-frame or pop-up
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