Depends which pass you have.. Normally if you live in Tokyo
city, you would have the MRT pass and not JR line pass unless you
frequent Yamanote line.
I did mention travelling time only didn't I? :P
Sometimes when I have to rush to Shinjuku or Shibuya from
Ikebukuro (as in really really rush) I will buy single trip and
take the JR.
Especially Shinjuku. It does take 5-10 mins to walk to
Shunjuku-Sanchome. Besides the entrance to the walkway is so
hidden.