Yes, that is a point we sometimes forget to mention. For some deluxe trains and shinkansens, seat reservations are either necessary or a good idea. To do that, you go to the JR ticket counter ("green window") at the nearest station, show your pass and get the seat tickets. You then show your Rail Pass as you pass through the manned gate to the right of the turnstiles to get to the platforms and show the ticket to the conductor on the train, along with your Pass.

For local trains or to sit in the non-reserved cars of the shinkansen, you don't need a ticket, just show the Pass as you pass through the manned gate to the right of the turnstiles.