Reserving tickets

Hi there!

Yes you would have to pay for the train in full if you want to reserve it before you have the JR Pass.
From other travelers I've heard that they successfully were able to re-book the ticket to the JR Pass.
You can do this by going to any JR Service Center with your JR Pass and ticket and ask the staff the refund your already purchased ticket and re book it using the JR Pass, do note that a cancellation fee applies.

A basic seat on the Hamanasu train is covered by the JR Pass but you will have to pay an additional fee if you wish to travel in a sleeping compartment.

Hope this helps!
Daniel

Thank you for your answer. Do you know how much for cancellation fee ?

Not exactly, it depends on when you cancel the ticket. Expect 500yen or so.