For my trip planning with trains in Japan i use http://www.hyperdia.com/
Excellent site and of incredible value for me, planning each leg of the trips.
However, the JR staff at the information and ticket sales counters are invaluable !!
They always understand what I mean and make reservations quickly and with a smile (make that a bow ha ha)
Today the ticket reservations clerk even notice a mistake I had made in my planning and saved me from an extra stop. Instead of 4 legs, he shortened my trip to 3, yet arriving at the same time and not really any big changes.
Here are today’s seat reservations, and by the way they don’t cost you anything when you have the rail pass unless you want to ride in the green cars, or I you want to take the EXTREME bullet trains: the Nozomi (which is not included in the JR Pass).
The Nozomi isn’t available everywhere. I’m thinking of taking one on Friday from Osaka to Tokyo … Just because I can lol