Japan Rail Pass

Hi. Our family of 4 arrives at Haneda on 28 June at 2230 and will stay near Shinjuku Station. We need to travel to Atami in the morning of 29 June and arrive in Atami by 1030. We need to leave Atami at 1243 to Takayama.
if I purchase a JR Pass, from what time can i activate it at Shinjuku Station on the morning of 29 June, since i will not be able to do this at Haneda when i arrive?
thereafter, is there a ticket office where i can get assistance to book our tickets and how early do i have to go to the station to make these bookings?
my concern is that i might not be able to get seats for that day to complete our travel to Takayama after stopping in Atami.
is it possible to reserve seats in advance , before we arrive in japan , if we have purchased a JR Pass, and what is the process to do this?
thank you