REI sells a great foam v shaped pad for your cross-bars. My problem is that the roof is really high (not a show stopper). If you have a long paddle and your arms are tired, sometimes it is a hassle to get it up on the roof. That is with a 31" tire and a 2" lift as well.
The foam pads and a couple of straps are great. If you go this route, just make sure you are placing your straps over the kayaks supports so it doesn't crush the Kayak if it is a composite plastic instead of a more rigid fiber.
Yep, I have a Sit-Atop Kayak, very flexible in all around use, but it is much heavier than your typical kayak and just like you say, its a huge pain to get it back on the roof of the Commander after a long paddle.
I have no problem using the factory crossbars for two Kayaks laid flat upside down on the bars. A 13' sit-atop that is a little wider than typical and a 10' sit-in. I can't get both side by side laying flat upside down within the width of the knobs on the ends of the factory crossbars (i.e. the knobs acting like a restraint to keep the kayaks from sliding off the side of the bars while cornering) one kayak has to lay over the knobs. BUT, the supports for the crossbars, that clamp into the roof rails, have openings in them, I found snaking the straps through the openings in those supports at the end of the crossbars works great, when you tighten down the straps they not only hold the kayak down tight against the bar, the strap being anchored at the end of the crossbars prevents any motion side to side as well.
This will all depend on the size of the kayak you going to put up on the roof, if they are big enough that both can't lay side by side with only a tiny bit of overhang of the roof rails, then yea, purchasing a kayak carrying system, where they are supported and anchored on their sides may be best.
But if the two kayaks will sit side by side, flat updisde on the roof, with only a few inches of over hang of the roof rails, the factory crossbars will probably be a lot cheaper and be perfectly secure way to strap down your kayak.
One other consideration, and this depends also on how detailed you are in preparing to mount your kayak on the roof. Seats, back straps, other straps and attachments will hang down while the kayak is upside down on the rails and it will only be 2.5" over the roof, so all these things hanging down from the kayak, if you don't tie them up and secure them, can bang against the roof during driving and even scratch the paint on the roof. The kayak carrying systems that mounts the kayaks on their side would be an advantage in this case. Again depends on the kayaks you have (i.e. do they have lots of things that hang off them, like my sit-atop, and how much time you want to spend tieing all that up).