Can I make reservations before JR Pass activation?

Greetings!
We arrive in Japan (Narita) on December 13 and depart on January 2. We will be spending time in Kyoto from December 24 through December 29. We then go Kanazawa for 1 night and then back to Tokyo. I know that the last week of December is very crowded on the trains and people start reserving seats a month in advance. Will we be able to reserve Shinkansen train seats well before we activate our 21 Day Japan Rail Passes on December 13? Or, do we need to purchase separate Shinkansen tickets online a month ahead and make reservations at that time?
Thank you for your assistance.