How do JR train lines work? (Kyoto)

I don't have commuter trains where I live in the US, so I wanted to make sure I understand the JR train system fully before I head to Japan. Pardon my ignorance, how do the JR lines work in terms of using the JR pass and traveling from one point to another?

If I have a pass, do I just wait for a train, show the pass and board (for unreserved); or do I have to use the pass to get special/specific tickets before I wait/board?

Also, do JR trains in Kyoto stop at each station along the way? For example, if I wanted to go to Nara or Arashiyama, do the trains going to these places stop at multiple stops until they get there? I'm wondering because I'd like to go to Nijo castle on the way to Arashiyama. And I'd also like to go to Byodoin on the way to Nara. So if I wanted to stop at those places, do I need to get on specific trains that go only to those stations (and not the ones that go to nara or arashiyama)? And if trains do stop at multiple stations, how long is a typical stop (do i just wait on the train?)?

Map: http://www.japan-guide.com/g5/2363_04.gif

how do the JR lines work in terms of using the JR pass and traveling from one point to another?

The pass is your ticket. You show it to the person at the manned ticket gates. Here are the basics:
http://www.japan-guide.com/e/e2016.html

If you want to use a reserved seat on long-distance trains, you should make a seat reservation ahead of time at a ticket office.

Also, do JR trains in Kyoto stop at each station along the way? For example, if I wanted to go to Nara or Arashiyama, do the trains going to these places stop at multiple stops until they get there?

Yes, they stop at multiple other stations. Also, there is no direct train between Nara and Arashiyama. You will have to transfer at Kyoto Station.

I'm wondering because I'd like to go to Nijo castle on the way to Arashiyama. And I'd also like to go to Byodoin on the way to Nara.

Nijo Castle is a ten minute walk from Nijo Station along the train ride between Kyoto and Arashiyama. All trains stop there.

Similarly, Byodoin is a ten minute walk from Uji Station along the train ride between Kyoto and Nara. All trains stop there.

And if trains do stop at multiple stations, how long is a typical stop (do i just wait on the train?)?

The typical stop is around 30 seconds.

Thanks, Uji.
I've been living on this site for the last couple of weeks in order to plan my trip. It seems like I learn something from you EVERY time I search these forums, and that's not including times you have helped me. Do you run this website??

JR Nara line takes you from JR Kyoto to Nara.

Kyoto, Uji and Nara are comparatively large stations on this line and all types of the train stop at these stations.
http://en.wikipedia.org/wiki/Nara_Line#Station_list

2 rapid types are operated per hour between 8am and 10pm.

All the trains on JR Nara line from Kyoto are not discontinued till Uji, but some local trains are discontinued at Uji or Joyo station. All Rapid types from Kyoto are bound for JR Nara.

Thanks, V.

I have another question about Nijo Castle. I think I read on here that the best route from Kyoto station is to take two subways and get off right at Nijo Castle. How long is the walk to Nijo castle from the subway stop nearby?

A 10 minute walk from Nijo train station doesn't sound so bad. Is there anything besides less walking that makes the subway a better option than taking a train?


Thanks!

It's less than quarter mile from the subway station(T14) exit to the Nijo castle entrance.

From JR Nijo station, you can also catch the subway(T15) to (T14). T14 is the nearest station from the castle.
http://www.city.kyoto.jp/koho/eng/access/subway.html

about Is there anything besides less walking that makes the subway a better option than taking a train?, yes, the subway is faster and more frequent, but it also depends on where you will be staying, i mean if you book a hotel in Gion, than taking the train to Nijo doesn't make sense

about And if trains do stop at multiple stations, how long is a typical stop (do i just wait on the train?)?, if you take a local train between Kyoto and Nara, the stops at some stations take much more time (5 minutes), to let pass the so called express trains (it takes about 80 minutes by local train and 45 minutes by express train to get from kyoto to nara...)

@V thanks for the subway link!

@Bert thanks, it's good to know the subway is faster and easier to access as long as you're near it. I will be staying at the Granvia hotel above Kyoto station for the convenience factor, so I should probably think about using the subway as often as possible... What I've been hearing about the bus system scares me. I Don't want to lose time because of traffic!

The buses look to get very crowded at peak times. If you are traveling in a group of 3 or 4, taxis are worth considering. They are very clean and while they are not cheap, they wouldnt compare too badly where there are 4 of you, as is the case with my family and I. It is unusual to have a trip for less than 1000yen (in fact 1030yen seems to come up a lot) in Kyoto it is also pretty unusual to have a trip for more than 2000yen, because most things are pretty close.