You will need some way to transport your boat on or in your vehicle.  This is easy if you have a pickup truck or cargo van as you can simply toss in the back of the vehicle.  Most paddlers use cars and these typically require a roof rack system of some type.  Although some paddlers can fit their boat inside their vehicle, I strongly advise against this practice.  I have seen too many accidents with this mode of transport.  If you take this chance, tie down very securely on both ends of the boat.  With any boat carrying system, imagine the consequences of slamming on the brakes at 70 MPH - those boats better be 100% secure.

Roof racks of some type are the best means of transporting your boat and your paddling partners on a shuttle.  If your vehicle has rain gutters - you are really in luck.  Quick-N-Easy rack systems can support several tons of weight and last forever: Quick-N-Easy Racks.  They are also the least expensive system - between $70 - $90.  Unfortunately, most cars these days don't have rain gutters and need more sophisticated systems.  The two major brands are Yakima: Yakima Racks which uses a round bar or Thule: Thule Racks which uses a square bar.  Each system has their fans and either will do the job.  One issue with both Yakima and Thule racks is carrying capacity, both top out at 200 pounds - 4 - 5 empty boats.  I strongly advise against loading wet gear in boats and carrying a bunch of them as this places a great strain on the rack systems they were not designed for.  Expect to shell out roughly $300 (or more) for either brand.

Another alternative for carrying a single boat is a foam system.  These systems are simple and quite cheap - between $5 - $50.  The foam protects your car roof.  Here are some examples: Alternatives.  In a pinch, you can improvise your own system using a blanket as well.  The trouble with this approach is you really can't carry more than one boat safely.

Whatever system you use, you need to secure the boat/s.  This is typically done with cam straps: NRS Cam Straps or rope.  Secure across the side of the boats with 2 straps or two ropes.  In addition, tie the front and back to your bumpers.  If the rack system fails (and they do from time to time), the front and rear painters will keep the boats from falling off the car long enough for you to stop safely.  Never use bungee cords for securing boats.  Bungee cords stretch over time and can come loose on bumpy roads.

Straps need to be tested every trip and cam buckle springs fail over time.  Always pull tight and straight down, never on an angle.  You also need to add an overhand not to prevent the strap from backing out if the cam becomes loose while driving.  Straps provide more friction than ropes which is beneficial.  15' is a good strap length.  Here is a good diagram that shows how to use your straps for securing a kayak: Kayak Strap Threading.

Personally, I am old school and like ropes.  Ropes are cheap and very versatile.  You will still need ropes to secure the front and back of the boats to your bumper.  Many boaters skip this extra precaution and many have lost boats when stopping suddenly - learn from their mistakes.  Rope systems also allow you to quickly add extra tie downs for more security.  When using rope, I really like 1/4" nylon over any other material (sisal, cotton, poly, etc.).  Get two 50' rolls, cut in half, singe each end with a cigarette lighter.  Add a Figure 8 Loop on one end.  Loop through your boat grab loop.  That takes care of one end.  For the other end, I start with a Truckers Hitch.  This knot allows you to really crank down on the rope and still untie the knot quickly.  After cranking down, you tie off with a Two Half Hitches knot.  I also like to tuck a cheap wash rag between the rope and hood to protect the car finish.

If you follow the above steps, you can drive like a mad man on jeep trails in heavy storm conditions and take comfort that your boats will stay on your car.  Trust me, that is a good feeling.