Hokkaido Rail Pass

Hi,

1) Can I exchange my Hokkaido rail pass at Haneda Airport or must I exchange it at Hokkaido (Hakodate Airport)?

2) Can I book the seats for JR train online in advance or can I only book at the ticket office when i'm there?

3) What happens if I book a seat on the train but miss the train? Can I still use the same ticket to take the next train or do I have to buy another ticket?

4) Can I use the Hokkaido rail pass to take any train (eg. limited express) or is there a specific type of train I need to use for the pass?

5) I read that the Hokkaido rail pass cannot be used on South Hokkaido railway. Does this means that I cannot use it for travel in Hakodate, Noboribetsu or Sapporo? So I have to purchase a separate ticket for South Hokkaido?

Thanks!

Can I exchange my Hokkaido rail pass at Haneda Airport or must I exchange it at Hokkaido (Hakodate Airport)?

No, exchanges are not possible at Haneda Airport, but you can buy the pass there.

Exchanges are only possible at designated railway stations in Hakodate. It is not possible at Hakodate Airport. Here is the list:
http://www2.jrhokkaido.co.jp/global/english/railpass/rail02.html

2) Can I book the seats for JR train online in advance or can I only book at the ticket office when i'm there?

JR Hokkaido has an online reservation system in English, but it cannot be used by pass holders:
https://www3.jrhokkaido.co.jp/rail-en/asp/RWY010.aspx

3) What happens if I book a seat on the train but miss the train? Can I still use the same ticket to take the next train or do I have to buy another ticket?

If you travel by regular ticket (as opposed to a rail pass), then you can ride a later train on the same day in the non-reserved section. If you travel by a rail pass, then the rail pass is your ticket. You could make another seat reservation. But if many foreign travelers continue dishonoring their seat reservations, the "free seat reservation" option will sooner or later be evoked or limited, just like JR Kyushu did this year.

4) Can I use the Hokkaido rail pass to take any train (eg. limited express) or is there a specific type of train I need to use for the pass?

Yes, all trains operated by JR Hokkaido except the Hokkaido Shinkansen.

5) I read that the Hokkaido rail pass cannot be used on South Hokkaido railway. Does this means that I cannot use it for travel in Hakodate, Noboribetsu or Sapporo? So I have to purchase a separate ticket for South Hokkaido?

"South Hokkaido Railway" is the English name of the railway company that operates a single, short train line between Hakodate and Kikonai. The Hokkaido Rail Pass' coverage area is explained here:
http://www.japan-guide.com/e/e2361_01.html