These both maps are Shinagawa station. ("KEIKYU" and "JR")http://www.ecomo-rakuraku.jp/stationmap/22709.htmlhttps://www.jreast.co.jp/e/stations/e788.html
The second map is "JR" only, but written in English.
Map top is West exit(西口 nishi-guchi), called 高輪台口(Takanawadai-guchi) as area name,
bottom is East exit(東口 higashi-guchi) called 港南口(Konan-guchi) also same.
You had to KEIKYU ticket gate(京急高輪口) on the 1F out from arrival platform on the 2F.
To go to the East exit again go up to the 2F and go through "free passage(自由通路)".
Certainly, the shortest route does not get down to 1F,
it is a way to go inside the ticket gate of "JR" through a transfer gate(のりかえ口),
but this method is not allowed because PASMO(IC card) causes an error.
The reason IC card causes an error is to prevent "unauthorized use",
so in case you like, you can correct the error as soon as you explain to the gate staff.
However, it is the answer to this question
that PASMO can not enter and exit only for shortcut ticket gates at the same station.
So, you understood that it is a long way to go via 1F,
but in Shinagawa station case this is the right way to use.
If in order to solve this problem, it is necessary to greatly renovate the station building,
it means to add a new KEIKYU ticket gate directly connected to the 2F passage.
But in this station transit passengers btw JR lines and KEIKYU mostly,
so this old structure still remains, it is inconvenient for some passengers like you.
there is no "subway(underground rail, 地下鉄 chikatetsu)" station at Shinagawa station.
KEIKYU main line is connected to the another company
subway Toei(都営) Asakusa line(浅草線) from "Sengakuji(泉岳寺) station" close to city center,https://i.imgur.com/CnMIayb.png
and many trains without transfer change are operated by 4 different rail companies cars
"KEIKYU(京急)","Toei(都営)","Hokususo(北総)" and "Keisei(京成)".https://youtu.be/mVcDJ8MOuJQ
Fares are the same for any train, no worry and Toei 5500 series(都営5500形) is the newest.
This is not a video recorded at Shinagawa, but you can see the brilliant of new cars.https://youtu.be/BDUSF18pc4U
This new car has only recently started operating in the KEIKYU ｌines section,
so it is very lucky to get on, but there is no guidance as to which company's car will come.
I do not know if you will come back to Keikyu Shinagawa station again,
but there is no train that Keikyu Shinagawa station will be the end,
so be careful of the destination(行先 ikisaki) of the train.
Departure info boards overhead of the the ticket gate
and platfome will display Japanese and English alternately.