If you plan to use a 7 day JR pass for a roundtrip from Tokyo to Kyoto (again returning within the 7 day validity) it pays itself off normally.
However there are other plans out there where you don't need a JR pass, for example sunrise tours:
http://www.japanican.com/sunrisetours
Offers Shinkansen roundtrip tickets PLUS hotel for a great deal
The JR Pass is only valid on JR trains (Japan Railways) and is not valid on subways/metros inside the cities. They are valid however on JR trains that operate within the city. A city like tokyo has subways(metros), JR trains, and other private rail.
Instead of doing two "day trips" from Tokyo, I would stay two days in Kyoto at least, the sunrise tour packages is actually cheaper then a JR pass, plus it includes accommodation, so something worth looking into.