This is a very interesting question. From where you will be staying in Tokyo the nearest stations such as Azabujuban and Kamiyacho are subway stations and you cannot use your rail pass when travelling from these stations. Tokyo subway stations have one or both of these logos on the map and at the entrance depending on the company which operates the line.





http://data.whicdn.com/images/204170631/large.jpg


JR lines in Tokyo are on this map. With a few exceptions (e.g. Narita Express at Tokyo Station) JR lines run overground in and around Tokyo. Unless you are going on a day trip to somewhere like Kamakura, it is unlikely they are the most convenient means of travel during your stay in Tokyo.



As abmj-jr points out most companies have separate stations or sections of stations. Don't worry too much about which line is JR and which isn't. If you try to go through a (staffed) gate at the station which is not for a JR line, they will politely direct you to a ticket machine. If you want to avoid having to buy tickets each time you might like to consider getting a Suica card each. It can be used in other cities such as Kyoto and Hiroshima on trains, subways and buses which are not covered by the JR rail pass.


Here is an entrance to the JR Shinagawa Station.



And a separate entrance to the Keikyu Shinagawa Station.