Reserving Shinkansen Seats?

Hi there!

I will be staying in Tokyo for 7 weeks, and then my mom is flying in for a week. We are planning on buying the 7-day pass to travel in Tokyo/Yokohama for 2 days, shinkansen to Kyoto for 2 days, 1 day in Nara, 1 day in Hiroshima, then back to Tokyo for another day. The last time I was in Japan I stayed on a cultural studies visa and was ineligible for the pass, so I had to book my shinkansen tickets through a travel agent. How do we use the pass to book shinkansen tickets? Can we book reserved seats on the shinkansen lines eligible for the pass without upgrading the pass? Do I have to do this in person at a station or can I do it through a site?

Thanks for your help!