I had to look up Myoko as I’d never heard of it! Also, I’m guessing you have a JR Pass rather than a JR East Pass? The JR Pass comes in 7, 14 and 21 day variants whereas the JR East Pass is a 5 day flex pass. Given that paying for regular tickets for your trip would cost under 20,000yen (USD178), you might find the 2 week rail pass was not a good purchase.
Either way, you can use it to travel from Narita to Shinjuku (using the Narita Express) and from Shinjuku to Myoko Kogen using the Shinkansen to Nagano and local trains from there.
Here’s an article on getting from Narita Airport to Shinjuku:
Also, the period that you’re travelling is a peak time for people in Japan so you should reserve your seat for Myoko-Kogen and even your return trip to Narita Airport as soon as you arrive. It’s quite possible that you won’t get a reserved seat for that period on the SHinkansen, but you can probably get a seat in the “non-reserved” section of the train. If you’re a bit unlucky, you might have to stand