Amanohashidate with JR trains?

hello,

me and my girlfriend we would like to visit amanohashidate on nov 30th.
hyperdia says there is a train at 9:35 (Ltd Express Hashidate 1) from kyoto to amanohashidate. can we use that one with our JR railpass and do we have to pay an extra fee? how do we do that as the train is a direct one?

thanks
snkfreak

Kyoto - [JR] - Fukuchiyama - [KTR] - Amanohashidate
http://backnumber.ktr-tetsudo.jp/english/access/

After Fukuchiyama not JR.
So add KTRs fare 1480Y(1380Y)/adult oneway.
(1480Y : reserved seat)
(1380Y : non-reserved seat)

Ltd Exp Hashidate[特急はしだて] direct to Amanohashidate[天橋立] sta.
http://ekikara.jp/newdata/detail/2701071/60995.htm
http://youtu.be/7zlTRgwvR_k [Kyoyto - Fukuchiyama]

Really very simple. Just stay seated in the train and a conductor will pass and ask you to pay the additional fare. Keep your JR Pass available because he might ask for it just to make sure that you are travelling legally on that train. You will just pay for the the non JR bit to Amanohashidate. Enjoy the place, it's great.