Reserving seats for JRPass holders with normal tickets

It looks like you have a few options, and it all depends on where you intend to travel in Japan.

JR East

If you're travelling on the JR-East network (so that's north Honshu), then it is possible to reserve tickets online, in English and in advance for normal ticket and Japan Rail Pass holders at the JR-East reservation site. Seat reservations are free for Japan Rail Pass holders, but in order to reserve online you'll still need a credit card which will only be charged in the event you fail to pick up your ticket at the JR ticket counter by 9pm on the day before you intend to travel. When you go to pick up the tickets you'll need to go to the ticket office with the Japan Rail Passes in order to qualify for the free reservation tickets.

Other JR Networks

For all other networks, you will have to do the seat reservations in person at the JR desk in the station. You will be able to reserve both your friends JR Pass seats and your normal ticket seats at the same time, and next to each other. The only snag here is that you'll not be able to book them before they arrive as you'll need their paper Japan Rail Pass in order to reserve the seats you want for free.

Hope this helps,

M