While you should be ok to wait until you are in Japan to make your seat reservations, there are no guarantees during Golden Week! If you can read Japanese, then I recommend you make your reservations online as soon as you can using [eki-net.com], which can be made with or without a rail pass.
Free reservations in the station must be made on presentation of your rail pass and must be made within the validity period of your rail pass. As you can specify the start of the validity period up to 1 month after the activation date, this should give you good flexibility to book your tickets in advance.
Hope this helps!