ANA Travel Pass 10,000 how does it work?

I am flying into Japan (Haneda).
I want to get a 7day JR Pass and go all the way to Wakkanai.
Can I fly from Wakkanai to Okinawa using the travel pass?

I am not sure how to book it and where to purchase it? I read the japanguide page and it is still in clear.

Please advise if I have to book the travel pass with my travel agent before my departure or how? I bought my Japan this online.

Is it possible to go by air from Wakkanai to Okinawa direct?

If you travel before 24 Oct 2015, you can use ANA's Experience Japan Fare, which is also 10800 JPY per flight and can be booked online:

http://www.ana.co.jp/wws/us/e/wws_common/promotions/share/experience_j...

As far as I know, there are no direct flights from Wakkanai to Naha, so you'll have to fly from Wakkanai to Sapporo or Haneda, and then fly to Naha. Either way, you'll have to take two flights, so the total cost will be 21600 JPY.

There are actually 3 fares from ANA - the first two are priced depending on what your international airline to Japan is (Star Alliance or not).
http://www.ana.co.jp/wws/us/e/wws_common/book-plan/fare/special/airpas...
http://www.ana.co.jp/wws/us/e/wws_common/book-plan/fare/special/visit....
http://www.ana.co.jp/wws/us/e/wws_common/promotion/experience_jp/

The good news for the first two fares are that 1) they follow your international baggage rules since they are conjunction tickets, and 2) for the second and any subsequent flights, you can make date changes (but not route changes) for free. The bad news is that there are blackout dates during peak times. You also must be ticketed before arriving in Japan. To book them, do it online or call them up.
For the Experience Japan fare, there are no black out dates (yay!) but there are no date changes or refunds.
As TxF noted, there are no direct flights all the way to Naha. Simply not enough demand for it. You'd need to pay for 2 flights to get there.
Frankly though unless you want to stop off and tour some places along the way, taking the train from somewhere like Tokyo to Wakkanai would be a huge waste of precious time - it'd take a full day just to get to Sapporo, and then another 5 hours from Sapporo to Wakkanai - about 1½ days completely murdered by sitting on trains. Given the cheap cost of flights, especially by low cost carriers like Jet Star and Peach, it simply makes no sense to take the train for such a long distance.

We did Okinawa Sapporo 2 years ago with Peach Air. It worked out well and lots cheaper than any other airlines. But needed to transfer in Osaka.
http://www.flypeach.com/home.aspx

Please advise if ANA travel pass can be booked online?
If I book with a travel agent, there is a service fee.

ANA agent on the phone said I can book online but I can't find the link. Anyone know?