If you have a car rack with small round or flat bars, place your kayak either upside down or on edge to lessen the chance of distortion. Foam pads can help prevent distortion. If you have specially designed kayak carriers as part of an aftermarket rack system, follow the rack manufacturer’s instructions. If possible, place the cartop racks under the boat's bulkheads, where the hull is strongest. If that is impossible, place the bars or attachments as close to the bulkheads as you can. Whatever the case, tie the kayak securely to the roof rack with straps or ropes, never shock cord or bungies. While you want your tie-down ropes to be secure, be careful not to make them so tight that you risk distorting the hull-shape of your boat.
As an additional margin of safety, loosely tie down the ends of the kayak by running a rope from the grab loops or security bars to the front and back bumpers of your car. Don’t leave your kayak tied to the top of your car for a long period of time unless it is in transport, and always remember that distortion created by improper storage or transportation is compounded by excessive exposure to heat.
Your local paddlesport shop can help you find a proper boat transportation system that fits your car and your budget.