A transfer gate is a ticket gate where a passenger can exit one railroad line or station and enter another in order to make a transfer.
In Shinagawa / Tokyo, you can exit the Tokaido Shinkansen zone of JR-Central and enter the zone of JR-East at one Shinkansen transfer gate, so you do not need to pass through an exit gate + an entrance gate.
Looking at the station map, it is hard to estimate the distance between the Tokaido Line and the Yamanote Line. I agree. But please note that Tokaido Shinkansen and Tokaido Line are different lines. The latter is a non-Shinkansen line.
In Tokyo, Tokaido Shinkansen tracks, which are Tracks 14 through 19, are beside three platforms on the 3rd floor.
The distance to Track 3 or 4 depends on which track your Shinkansen train arrives at, but generally this transfer may need about 5 to 10 minutes, not including time on waiting for an elevator, an escalator or your JR-East train.
: The tail end of your Shinkansen train (from Shin-Osaka) is closer to the south concourse.
: Each of the three Shinkansen platforms is equipped with one elevator.
: You can get down to the south concourse on the 1st floor (= the ground floor), using this elevator or a nearby escalator.
: Then you can pass through Shinkansen South Transfer Gate.
: Walking a little, you see signs of Tracks 9 and 10 (for Tokaido Line) on your right, and you see a wide staircase with a few slopes in front of you.
: Then you can go down the staircase / one of the slopes and proceed on the pathway to an elevator, which can bring you up to the platform of Tracks 3 and 4. Alternatively you can use a nearby escalator.
I actually need to buy a PASMO Card before taking the train to Ueno. Basically it is not necessary to buy an IC card in Shinagawa / Tokyo when you travel from Osaka / Shin-Osaka to Ueno.
If you travel this way with regular JR tickets, you can get issued a basic-fare ticket which should be valid (at least) to Ueno Station + a Shinkansen super-express ticket. At a Shinkansen transfer gate in Shinagawa / Tokyo, you can put the two tickets together into a gate machine, each with the top side up, and the basic-fare ticket is returned while the Shinkansen ticket is collected.
A JR basic fare to get from Osaka / Shin-Osaka is at the same price regardless of whether the destination station is Shinagawa, Tokyo or Ueno. It is not necessary to pay a fare separately for the JR-East leg.
If you travel this way with a Japan Rail Pass, in which case you cannot choose Shinkansen "Nozomi" service, you can use that JRP (at least) until reaching Ueno Station. A Japan Rail Pass cannot be accepted by a gate machine, so you should show your JRP to a JR attendant when you pass through a ticket gate.
An IC transportation card (such as Suica and PASMO) does not give you a discount in particular, but it can save your time and trouble on handling cash and short-distance tickets.
You can have a chance to buy a Suica Card issued by JR-East outside ticket gates in Ueno Station of JR-East or, a PASMO Card outside ticket gates in Ueno Station (G-16, H-17) of Tokyo Metro subway.
A Suica Card and a PASMO Card work the same on the Suica-PASMO network in and around Tokyo, so it is not necessary for you to buy the both.
- Map of Ueno Station of JR-East
http://www.jreast.co.jp/e/stations/e204.html- Map of Ueno Station (G-16, H-17) of Tokyo Metro subway.
http://www.tokyometro.jp/station/ueno/yardmap/images/yardmap.gif: In the map you see escalators above Ginza Line tracks, which connect the subway concourse and the JR main entrance just near Central Gate.