SpaceShipOne made it!

[geoschmo]

And from the official X-Prize rules:

3. The flight vehicle must be flown twice within a 14-day period. Each flight must carry at least one person, to minimum altitude of 100 km (62 miles). The flight vehicle must be built with the capacity (weight and volume) to carry a minimum of 3 adults of height 188 cm (6 feet 2 inches) and weight 90 kg (198 pounds) each. Three people of this size or larger must be able to enter, occupy, and be fastened into the flight vehicle on Earth's surface prior to take-off, and equivalent balLast must be carried in-flight if the number of persons on-board during flight is less than 3 persons.

http://www.xprize.org/teams/guidelines.html

So, no, they don't have to have three people onboard, only be capable of flying with three people, and no, this flight won't count as one of the two flights needed for the X-Prize.