we had the handler arrange our trip down to machu picchu. from cuzco it's about a 4 hour train ride, then a 20 minute bus ride from the town to the ruins. the handler also got us a guide who showed us around.
i think if you were to go commercial down there, you would go via lima to cuzco. 3 airlines run out of lima; taca, star peru, and lan. i would pick taca or lan, as they were bringing airbuses up there, where as star peru was running about the oldest 737s on the planet.