Burt didn't use any wind tunnel testing for SpaceShipOne or hardly any other of his designs to the best of my knowledge. He has used CAD and custom programs dating back to the Apple II days. Of course, the computers and tools are much more powerful today. Watching the excellent Discovery Channel documentary "Black Sky" (highly recommended DVD purchase), Scaled's chief aerodynamist appears to use some form of computational fluid dynamics program for initial work. Burt also used small, hand thrown models to test various ideas like his shuttlecock mode.

Once he's satified with the basic concept, Burt then builds the vehicle and begins flight tests. With 40 years of flight testing experience (Burt was a flight test engineer for the Air Force from 1965 through 1972), they know how to conduct a good test program. Based on the test results, they make modifications as necessary. SpaceShipOne's maiden drop test was one of the most dangerous flights they'd ever conducted up to that point because they'd never had the opportunity to do any actual flight tests before dropping it live for the first time (from about 51,000 feet, no less).

Later flights showed that they needed to change the design for the control surfaces (a not uncommon event in homebuilt aircraft development), so Burt went back to a tried and true technique that he first used over 30 years ago when designing his first homebuilt plane (the VariViggen) - they mounted test surfaces on a truck and drove at high speed while taking measurements. In less than 2 weeks, they tested dozens of variations until they hit upon the final design. It worked like a champ.

Of course, I'm sure they compared their flight test results to the CFD predictions, but Burt is definitely a build and test kind of guy. CFD can get you in the ballpark (it was used to design the Pegasus air launched booster back in the 1980s), but there's no substitute for testing actual flight hardware and validating the CFD results. For SpaceShipTwo, they plan on conducting at least 50 test flights before carrying any paying passengers.