When to reserve seat

Hi, we plan to buy a 7 day JR pass but only to use on the fourth day upon our arrival. Therefore I plan to activate it in Shinjuku Station in the morning, before we depart to Hakone. As I prefer to reserve seat so the four of us can seat together (we travel with two children), I wonder if we can reserve seats before we activate the JR Pass? If must reserve seat at the same time with activation, will there be a risk that we will not be able to sit together (we travel in midst of June)? Thank you .