Q: Can I set up a separate passcode for use of facetime

iOS- Understanding Restrictions (parental controls)

iTunes- Using Parental Controls

iBooks and iBooks Store- Parental Controls in iOS 6

It would be a very good idea to read the links that Kappy posted above. But for a brief explanation .....

You can restrict FaceTIme in the settings and the app will disappear from the iPad as will the camera app. You will have to set a restrictions passcode if you want to do this. If you do set restrictions - do NOT forget the pascode or you have to totally erase the iPad to bypass the code. And most of all, don't share the code with the kids.

Settings> General> Restrictions> FaceTime> Off.

You can also block other users from calling in. Settings> FaceTime> Blocked> Add New.

Other than that, you cannot passcode lock FaceTime. There is no way to set a passcode in order to use the app, but you can restrict it as I explained above.