Tokyo - Kyoto

Hello,
We are traveling to Tokyo for 10 days. Here's our itinerary:
1) Tokyo Shinjuku May 31-June 4
2) Disneyland June 4-6
3) Kyoto June 6-9 (one day in Osaka but not stay overnight)
4) Kyoto to Narita June 9-10
5) Narita fly home June 10

I was going to buy the 7 day pass for our train ride to Kyoto. This is the most economical, I think. How do I activate it on June 6 when we leave for Kyoto? Can I do that at the Tokyo Station that day?

Thank you,
Joyce