I booked the VATICAN MUSEUMS AND SISTINE CHAPEL tour through the Vatican for a tour March 2008. From the e-mail receipt:

The guided tour lasts two hours and the rate includes the admission ticket.
Tickets must be purchased only on the day of the visit at the Vatican Museums "Guided Tours" desk.
To avoid any queue, you are allowed to enter the Vatican Museums from the entrance side, at Viale Vaticano, 30 minutes before the tour leaves.

As you can infer, I didn't pay ahead of time (apparently you did?), just made the reservation, then paid for the tickets when we arrived at the museum.