Assuming you have one rack mounted over the doors you should be able to secure things with two bow lines, and two stern lines.

The single mount will keep the boats from sliding off the roof, and the lines will keep them from twisting sideways.

If you make a "mount" for your kayaks which allows you to strap them together so they can be considered one unit, then you may find life easier. consider something like a couple pieces of plywood cut to the shape of each hull, and well padded. Put these between the boats, tighten the straps and you have one unit of two connected boats.

You can add to this.

A soft pad resting on the car roof behind the crossbar, but attached to it so it doesnt fall off, will provide a soft cushion to support the weight of the boats on the roof of the car. A piece of foam rubber about 4 to 6 inches thick should be idea. Maybe you can recycle a cushion from some old sofa by wrapping it in a piece of canvas, and then stapling the ends of the canvas to the crossbar.

There are bicycle racks which mount to the lid of the trunk, using straps and metal clips. if you can find one of these, use it as a base, and build up from it to create another support bar. You can bend some U shaped pieces from electrical conduit and connect them to the bike rack with stainless steel hose clamps to get the additional height.

And of course the trailer hitch receiver idea has been mentioned. But if you have a trailer hitch, then spend a few bucks and get a trailer. It will be a great investment as you can use it with any car, you can load up more than two boats, your paddles and other gear can store with the boats, and you are always ready to pull it out and go paddling.

Hope this helps

PGJ