Transfer gates while using IC cards

Hello everyone,

I have a question about transferring between Shinkansen and regular JR trains in different cities. To be as clear as possible in my question I'll use an example trip I'm planning to take.

While in Japan I will buy an ICOCA card at KIX. My Japanese friend travelling with me has a Pitapa card already.

Later we will take the Shinkansen (Nozomi) from Shin-Kobe to Tokyo Station, and then take the Yamanote Line to Ueno. Here's where I have a question.

-We will already have paper reserved Shinkansen tickets (base fare and supplement fare) on hand when beginning our journey. These are round-trip tickets from Shin-Kobe to Tokyo.
-Presumably we will use our IC cards to take the subway to Shin-Kobe. Once there, I assume we will tap out of the subway with our IC cards, and then use only our paper tickets to enter the JR zone and then the Shinkansen zone--is this correct? Basically, we put our IC cards away once we get off the subway? (Also, does anyone know where I can find a map of Shin-Kobe station?)
-Once in Tokyo the station map seems to put us in an interesting situation. I understand the Shinkansen transfer gates will eat our supplement tickets and let us out into the regular JR zone, where we can catch our Yamanote train to Ueno. We should still have our base fare tickets to let us out of the station itself, but we aren't going to exit the station! What do we do now?
-I guess we could buy another base fare to Ueno at the Midori no Madoguchi inside the JR zone. The purpose of that would really just be to allow us to get out of the station at Ueno, right? But what if we wanted to use our IC cards...would we exit Tokyo Station first and then tap back in with our IC cards before proceeding to the Yamanote Line?
-Similarly, what if we used our IC cards to get back to Tokyo Station from another place on the Yamanote Line? If we didn't tap out at Tokyo Station and re-enter using just our paper return tickets, would we basically be charged twice for travelling back to Shin-Kobe, once with our paper ticket (already purchased) and once on the IC card? How would the IC system know how far we travelled though, if all we did was say tap in at Shinjuku and then used our paper tickets the rest of the way, including to get out of the station at Shin-Kobe?
-Or, did we make a mistake buying both base and supplement paper tickets, if we also plan to use IC cards? Could we actually use our IC cards for the whole base fare from Shin-Kobe to Ueno or Shinjuku to Shin-Kobe (on the return trip), and then just buy the supplement/reservation tickets on paper?

Thank you so much for all your help. It would put my mind at ease to understand some of this better. :)

Presumably we will use our IC cards to take the subway to Shin-Kobe. Once there, I assume we will tap out of the subway with our IC cards, and then use only our paper tickets to enter the JR zone and then the Shinkansen zone--is this correct?

Yes, that is correct.

(Also, does anyone know where I can find a map of Shin-Kobe station?)

It is an extremely straight-forward station, but it takes about five minutes to walk between the shinkansen and the subway platforms:
https://www.jr-odekake.net/eki/premises.php?id=0610156

Once in Tokyo

Usually if you buy a ticket from Kobe to Tokyo, it allows you to get off at any JR station along the Yamanote Line or even in the 23 city wards. Check your base fare ticket and see what it states as destination station.

Even if it does not allow you to get off at Ueno, don't use the IC card. Instead, go to a fare adjustment machine at Ueno and pay the eventual difference there.

Not "usually": a base fare ticket from Kobe to Tokyo will always be from the Kobe city zone to the Tokyo city zone.

By the way, this also means that if you are leaving from another JR station in Kobe, you don't need to separately pay the fare to Sannomiya, this is included in your ticket (but the subway fare from Sannomiya to Shin-Kove isn't, of course).

Not "usually": a base fare ticket from Kobe to Tokyo will always be from the Kobe city zone to the Tokyo city zone.

There are some exotic cases in which the base fare ticket will be to/from a specific station within Tokyo rather than the 23-ward zone.

By the way, this also means that if you are leaving from another JR station in Kobe, you don't need to separately pay the fare to Sannomiya, this is included in your ticket (but the subway fare from Sannomiya to Shin-Kove isn't, of course).

I understand that you have to use special ticket gates or manned gates in order for the ticket gate at Sannomiya Station not to consume your ticket.

So, is it okay to ride to Ueno, knowing full well that I don't have sufficient fare to get out once I arrive? Are you supposed to travel planning to use a fare adjustment machine at the end? In any case I hope it is true that a Shinkansen ticket would cover me to any JR station in Tokyo. :d

There are some exotic cases in which the base fare ticket will be to/from a specific station within Tokyo rather than the 23-ward zone.

Such as? I am not aware of any exception to the general rule in Tokyo.

So, is it okay to ride to Ueno, knowing full well that I don't have sufficient fare to get out once I arrive?

Yes, that is okay. But as mentioned above: you will most likely have a ticket that covers your ride all the way to Ueno.

Are you supposed to travel planning to use a fare adjustment machine at the end?

It is not the ideal case, but sometimes it is the most practical. And it is not against the rules.

In any case I hope it is true that a Shinkansen ticket would cover me to any JR station in Tokyo. :d

It most likely will.

Such as? I am not aware of any exception to the general rule in Tokyo.

If you were to enter the 23-ku area once, leave it again and then re-enter it. There may be other exotic cases.

Right, and the same idea applies for the departure zone (if you exit the departure zone, then re-enter it before proceeding to your destination). Such itineraries are very unlikely to come up "naturally", however.