The first step in tieing your canoe or kayak down to your car is to lay the kayak straps over each bar. Thread each strap underneath and around each bar and let the kayak straps lay flat against your vehicle. Of course you will want to make sure the clamps on the end of the straps don't scratch your car door. The best way to avoid this kind of damage is to pull the end of the kayak strap that has no metal on it longer than the end with the clamp. Allow the clamp to rest against the window.
If you haven't already done so, it is a good idea at this point to check the crossbars of the kayak rack. Make sure they aren't loose. If they are, tighten them. Each rack will vary but they usually just require an allen wrench to tighten them.