Bukkit is a third party server tool, which means its not supported by mojang, but many people use it and will offer help by directing you in the correct direction.
To make a bukkit server using factions, you would need this Factions 1.6.1
Just follow the installation instructions. Should be simple enough.
mojang give the code to the bukkit team before offical release and i beleive bukkit have passed on many of their own bug fixes back to mojang to impliment.
so i wouldn't call it unoffical in all aspects, though the bukkit team do not get paid by mojang.....yet, its only time before they join forces.
this is a nice guide on how to start a bukkit server