First visit to Japan!

Greetings!
Ive been browsing internet for endless hours every night reading up on trains and how to get around in Japan and still there is many questionmarks!

We are 2 adults visiting Tokyo for the first time!
We where thinking about visiting Kyoto from Tokyo one day and stay over night, then return to Tokyo. Except for that we intend to stay in Tokyo for the rest of our visit. So im alittle confused about all the options when it comes to the public transportation. Is it really worth getting a 7D pass for 2 people when we are only gonna do travels within Tokyo and a trip/return to Kyoto ?
If not, what options are there IN Japan? or do we need to have all trainroutes planned out before even arriving?