A good preparation will help you make the most out of your Vatican visit. Knowing that it is impossible to see all the interesting sites and pray in all the beautiful churches, you will need to choose some, and let others wait for your next trip. Your choice will depend on the number of days you plan to come, group size, transport, walking stamina, and so on. The best would be to first target places you really want to see, and then check online for the experiences of other visitors. This way you could decide on your possible routes, based on your particular situation, and even think of alternative plans.
Usual places to visit in the Vatican (please reserve directly through their contact numbers and/or emails, not through the Collegio):
> Scavi or Necropolis (ancient cemetery) under the Vatican Basilica (don’t miss this! though you have to reserve months ahead due to the limited slots)