The ideal way to secure a long skinny thing of any sort on top of your vehicle or trailer is to run a total of four separate lines from the front and back of the object to the front and back of the vehicle, forming an inverted "V" at each end. These lines should be slightly snug, but not tight, especially if you are carrying a rotomolded plastic kayak.
If you are carrying two kayaks you'll need twice as many bow and stern lines, making two asymmetric "V" shapes at each end.
You should also use two belly straps per boat, using cam straps and NOT ratchet straps. The belly straps should be run to make a continuous loop in the form of an inverted "U" with the ends going around the load bars of the roof rack and the "U" going over the boat.
Ideal attachment points for bow and stern lines are "Hood Loops", sold at a kayak/canoe shop near you. You can also get "Rope Ratchets" and "Cam Straps" from the same folks. If you choose to use Rope Ratchets make sure you drill out the pin holding the hook and replace the hooks at both ends with carabiners so the hooks can't come undone on rough roads.
And now for the rationale for all this:
Secure lines and straps keep boats on your car.
Overly tight lines and straps crush and deform your boats - especially plastic kayaks.
You can have secure (just snug) lines going to all four corners of your vehicle and withstand insane windloads - I have personally driven through windstorms with my 17' wood touring kayak on top of my car at upwards 80MPH road speed - diagonal wind speeds exceeded Cat 2 hurricane conditions. The kayak was on foam blocks set on Thule loadbars, the front and rear tiedowns were as described, as were the belly straps. The kayak pivoted up to six inches from side to side a couple times, but remained very securely attached to the car. It works. In calmer conditions I've had my tandem canoe up over 90MPH with less dramatic results - it just sits there.
Photos of stuff:
Hood Loops

Hood Loops Installed

Cam Straps

Rope Ratchet - 1/4" version
