Timetable and seat reservation

Hi,
My son and I have planned a trip to Japan. We will fly to Narita, stay in Tokyo for some days, then go to Kyoto. After some days we will travel from Kyoto to Narita airport where I booked a hotel for the last night. I have already bought a 7-days railpass. It should be activated the day we leave Tokyo to Kyoto.
My questions: Where do I find departure information for the different distances on the trip: which railway station (I guess there ar many in Tokyo), which train/ line and the timetable.
Do I need to make seat reservation an advance? How can I make the seat reservation - do I need to go the railway station in person for that?

Kind regards
B