The Inno IN-SU roofrack system is a great match for a 2006 Honda Civic 2 door roof rack to transport surfboards. The Inno IN-SU uses Fit Hooks that match the exact contour of the vehicles roof edge and upper door wells for a very seamless fit and will not affect the car's finish. The 2006 Honda Civic 2 door uses the Inno K552 Fit Hooks. The IN-SU roof rack comes with locks included soyou can lock the car rack to the rooftop. Also the IN-SU is available in both black and silver color options.
http://www.orsracksdirect.com/inno-in-su-roof-rack-system.html (black)
http://www.orsracksdirect.com/inno-in-su-car-rack-silver-system.html (silver)
You will also need to use the Inno IN-JK Joint Bar adapter kit in combination with the Inno IN-SU roof rack system. The Inno IN-JK Joint Bar kit is designed for cars with short roof lines and enables the front and rear cross bars on the IN-SU to be spread further apart from each other so you have a very stable and safe platform to then attach the gear carriers such as a surfboard rack.
http://www.orsracksdirect.com/inno-in-jk-joint-bars-kit.html
The Inno INA744 BoardLocker surfboard rack is an amazing carrier. Attaches directly to the IN-SU base rack system cross bars and includes an integrated locking system to lock the surfboards to the rack. The Inno INA745 Crane surfboard rack is another great option that is less expensive but does not offer locking capability.
http://www.orsracksdirect.com/inno-racks-boardlocker-surfboard-rack.html
http://www.orsracksdirect.com/inno-ina745-crane-board-carrier.html