The most cost effective rack system I have found and the easiest to load and unload without breaking the bank is:
Thule Towers (to fit your factory rack) mine have a rubber belt that clamps around my rack and tightens with a built in allen 'T' wrench. I added the key locks and the two racks are fully removable when not in use.
Thule 65" square bars
Yakima Land Shark Saddles
Thule Water Slide mat
I carry two Revolution 13's side by side and upright.
Simply lift the bow onto the water slide and grab the stern and slide it up onto the saddles. Put a pad, PFD or carpet under the keel if dragging the yak along concrete when getting bow up onto vehicle.to avoid sanding down your keel.
This will keep you under $500.00