I have been out of the kayak scene for some time, but this is my 
take on the subject.
I kayak fished once a week for two solid years in Southern 
California, my routine transport distance 30-40 miles from LA to 
Malibu or Ventura....part highway, part major route.
All I had was a regular thule roof rack  and not a kayak specific 
rack.  I got the advice from a bunch of experienced guys.  There 
are a number of cradles and roller systems out there, but they 
really are not necessary, and they also seem to make it more 
difficult to carry multiple yaks on the car.
You can pick up thule/yamika racks on craiglist pretty cheap if you 
are on a budget...and just buy the kit that is appropriate for your vehicle.
Transport the kayak deck down...if the deck deforms a bit no 
problem....if the hull deforms then you have a warped hull.  You 
don't want to warp the hull, so transport pressure should be on the deck. 
Strap down the bow and stern to the front and back of the car. 
Just make sure what you tie it to is sturdy. I hauled my 14' xfactor 
on my vw jetta.  The car had a brass tow link that I could thread 
onto the chassis through a window on the valance. In the rear of 
the car there was a permanent tow link.  Strap down the mid 
sections to each local roof rack cross bar. Done.  
the straps I used...are under 15 bucks...and look something like 
this...you can find them at homies/lowes....If you can find ones that 
are rubber coated...it is better so they don't ding the paint.
For a second kayak, lean it against the longer, and strap it down 
the same way.  Me and my buddy would drive 120 miles from LA to 
LaJolla that way.  It ain't pretty but it gets the job done fine.
I hope you find the advice useful.