Got the JR pass 5 years ago when I last went. It was totally worth it and includes JR lines in Tokyo IIRC. But come again this time and they have increased the price so it was not worth it. So got separate fares instead. You need to go through with two tickets - fare ticket and express ticket and put them through the barrier before going onto the Shinkansen. If you’re going to multiple destinations like we did - Kyoto, Osaka, Hiroshima and then back to Tokyo then there can be multiple tickets and can get confusing. Just check you have them all before leaving from Tokyo.