Online seat reservations with purchase through JRPASS

Hello, we are a little confused on the ability to reserve seats online. We would like to purchase our pass through your site, but we would like the ability to reserve seats online and just pick up the seat tickets from the machine before departure. I have read that we can only do this online seat booking if we purchase the pass through the main JR site.
We will be starting in Tokyo and travel to Kyoto, Kobe, and some other destinations in the south for 14 days before returning to Tokyo.
Can someone please advise about the ability to reserve the seats online?
Thanks in advance,
Rick