Speaking from the perspective of leaving Tokyo in just a few hours...
When you purchase the Nex r/t ticket, you are given a voucher for the return. It has a relatively broad length of time it is good for. When you know your departure date, go to a JR Service office with the voucher(s) and they will set you up for the actual ticket for the return. The reserved seats are included in the price.
Enjoy your trip!