Probably if you were only going to do a trip Tokyo <> Kyoto/Nara/Osaka, then a 7 day pass will be good for you, not a 14 day pass. If you think you'll do more long distance travel (eg, trips to Nikko or Hiroshima), then maybe could recommend a 14 day pass, but it would really depend on how much extra travel you're planning on.
For changes from JR stations to Metro, it also depends on the station :). Many stations, like Tokyo station, have integrated Metro and JR lines running through them, but in all cases you'll need to leave the Metro operated area and enter the JR operated area through ticket gates rather than simply changing platform. If you let me know which station will you be staying near to I'll see if I can find more detail for you.
Hope this helps!