Tokyo to Tokamachi and Tokamachi to Nagano with a JR Pass

Hello! I bought a JR Pass from this same page and I will be going to Japan in february.

I want to go to Tokamachi Snow Festival, and then go to Nagano to see the snow monkeys. For this I would have to do:

1) Tokyo to Echigo Yuzawa and take a train on Hokuhoku line. Part of this (until Muikamachi?) uses JR Joetsu Line railways so it should be covered in JR Pass as I understand, and another part goes through non-JR lines.

2) To Nagano, use the JR Iiyama line from Tokamachi up to Nagano, but from Toyono to Nagano uses a non-JR line railway so I should pay a supplement fee.

The question is how I pay this extra fees? Can I pay in the train? because Hokuhoku doesn't use a conductor, is only a driver, don't know about Iiyama line. I have to buy a separate ticket in a machine previously? Can I buy this tickets from a machine from, say, Tokyo before going there? Or for Toyono-Nagano in Tokamachi? How this works?

Thanks!