Having just done TozoiLine>ToykoStation>Kyoto>Shinagawa>NRT I'll post a few observations here.
Like other posters I had done considerable research, including figuring out which platform I needed to be at for each train, station maps, etc. NONE of it was necessary!
Every station was clearly signposted, and in every case the Shinkansen platforms were through a separate entrance with a signboard that showed which track each train departed from. There were directional signs every few feet in the stations - in some cases directing you in multiple directions when there were several entrances. Once on the platform, there are clear indications of where you need to stand to wait for each car. Ditto when you need to transfer, the platforms were clearly posted to indicate which exit to take for which trains.
General observations:
The transfer at Tokyo was much harder the the one at Shinagawa for someone who was doing it for the first time. Tokyo is HUGE and every part I was in was like a huge underground shopping plaza that looked like a habitrail. Even so, the Shinkansen entrances were very clearly signposted everywhere, including all the way from the Tozoi station, which was a couple blocks away.
At Shinagawa I only had to go up from the platfrom (escalators/elevators available) and then back down to the other platform for my next train. Much easier than at Tokyo. If I had my choice I would certainly choose Shinagawa over Tokyo.
The only mysterious thing for me was how the tickets worked. I was doing TOKYO>KYOTO>NARITA (NEX) and my got the tickets through a corporate travel agent and was just handed an envelope full of tickets. I had four tickets - one for TOKYO-KYOTO, one for KYOTO-SHINAGAWA, and one for SHINAGAWA-NARITA. The fourth I assumed was a receipt since it didn't have any train information on it. When I used the first one at TOKYO the gate opened and I got the ticket back, stamped. When I used the second one at KYOTO the gates didn't open and an agent came over when I looked confused. She retrieved the ticket from the machine and said "you also need the other one". I rustled through my envelope of tickets and she took out the one that I thought was the receipt and had me put both of them through the machine. They both came back out, one stamped and the gates opened. When I got to SHINAGAWA I put them both in the machine and it seemed happy. I have no idea why I needed only the one the first time, but both the second.
But, general advise is to just plan on arriving at the station a little early and to take your time looking over all the signs. Everything is there but it can certainly be overwhelming the first time. Even as a non-Japanese speaker I had no problem. 99% of the information was in Japanese only, but the 1% you really needed was also in English.