I don't have a handbook for you, but one thing that I think is important is to have some form of "check-in" with the intern throughout the course of the internship. It could be weekly, or at the beginning and end of the internship, or after every show- the frequency might be determined by the length of the internship.
Having a check-in allows you to ensure that the intern is getting an educational experience, and identify any potential issues with them before they become big problems. It allows you to hear from them about their experience- what they are having trouble with, what they're enjoying, what they would like to learn more about, etc. It also allows you to give them constructive feedback, and adjust their responsibilities and assignments accordingly.
I also think it's important to have them keep a timesheet, so that there is an accurate record of hours worked.
One theatre that I worked at did a bi-weekly staff meeting, and at the end of the meeting we had the interns tell us what they were working on that week, and what outside shows and projects they had going on. It really made them feel like a "part of the team" and the staff was always happy to hear about their work.