I know that the show is supposed to take place in a convent in San Juan, Puerto Rico, but was it also filmed there? If not, where then?

I can't be sure of all of the locations. perhaps there were more. The convent scenes, were flmed in puerto rico. My guess only

No, the convent scenes were filmed at the Columbia (now Warner) ranch, along with exteriors for other Screen Gems series of the time ("Bewitched", "Jeannie", "Partridge Family", etc. Check out this link (http://www.cmongethappy.com/people/ranchtour4.html) -- part of the convent set is still standing at the ranch.