How to reserve JR seats, if

...we will catch train to Kyoto immidiately after arriving to Tokyo? I understand it is not possible to make reservation from abroad?

At the ticket counter of Narita Airport Station. On normal days, the trains are unlikely to be booked out. If the train to Kyoto is booked out, you can still try to get a seat (or stand) in an unreserved car.

Obviously your concern is getting your train seat reservation from Tokyo to Kyoto which takes about 2hours and 45 minutes. We've done this before without advance reservations. After customs, immigration and baggage claim we exchange our JR Rail Pass Order for our JR Rail Pass. We get our train tickets at he same time.

JR Service Center is down the escalator in the Arrival Lobby as you exit baggage claim. We catch the NEX-Narita Express to Tokyo Station allowing at least 20 minutes for transfer to our Shinkansen train to Kyoto. NEX from Narita to Tokyo takes about 1 hour and usually has a number of empty seats.

Thus far, we've always managed to get reserved seats on NEX and the Shinkansen without advance reservation. If by chance no reserved seats are available on your choice of Shinkansen train, the next train leaving about 30 minutes later should have reserved seats available. You can also get onto the unreserved seat car but surely you'll be able to get on the train. Still, it's unlikely that reserved seats will be 100% booked.

I can see where you can be stressed in trying to get reserved seats especially if your arrival time at Narita Airport is in the late afternoon or later. Then you don't have the option of catching a later train. Flight arrival at Narita before 13:00 (1:00PM) would be ideal for less stress commuting to Kyoto. So, I wouldn't worry about advance seat reservation before you get into Narita.

Tnx, your answers give me some peace about Kyoto trip:)