After reading all the idiots guides to the JFK Air Train I still managed to get confused. As I seem to be a new breed of idiot I thought I would list how I used the AirtTain and hopefully it will help others,
After collecting luggage follow the signs for the AirTrain, once at the station look at the TVs above the doors. Each AirTrain either goes to Jamaica Station or Howards Beach, the TV above the doors tells you what is next. You don't pickup a ticket or pay anything before you get on the train.
We caught the train to Jamaica Station, once you get off the train you will notice the barriers, you need to buy a ticket to exit. There are lots of machines just before the barriers. This is where our first mistake came, we thought you could buy a MetroCard, top up $5 for the AirTrain and also add the 7 day metro to the pass. It turns out you can only add value to the card from these machines so if you are just paying as your go on the Subway you are OK.
After a lot of messing around we asked a helpful employee who explained that we can not add unlimited ride passes to the MetroCard purchased from those machines and that we need to top-up downstairs at the MetroStation. So we purchased 2 cards at $6 each ($1 new card fee and $5 for AirTrain fare).
We walked downstairs to the Metro station and made our second mistake and inserted our newly purchased cards from up stairs and found we could not add unlimited rides. It turns out we had to buy another MetroCard for the subway so we ended up with 2 cards each. Its no problem as we used the AirTrain one on the way back.
Just thought I would let everyone know so you are not going round in circles on the Metro machines looking for the 7 day pass option.
Have fun everyone.