It’s very easy these days. Apple Maps can tell you exactly where to go including platform and boarding time.
Paper tickets are confusing but basically nobody uses them. I don’t think it’s true that you need to get separate tickets for separate train lines. You do need to adjust your ticket if you prepaid the wrong distance.
Unless you mean two entirely separate lines separated by different gates.
There was a station (which I don't remember) I had to leave the subway and buy a different ticket to transfer. Some stations have multiple platforms stacked next to each other that it is easy to transfer even if the lines are managed by different railway companies, but that is not the case all the time. That's how I learned that there are multiple railway companies in Tokyo that are not cooperating with each other enough to make the transfer seamless. Once you make a few mistakes, it gets easier, but it is not so friendly to foreigners. Also stations like Shinjuku is so huge that it is very complicated figure out where your exit is. Then again, once you get used to it, it becomes easy.
You might have to switch to, say, a JR train line. But that’s not a function of the paper tickets. Just different lines. Honestly the much crazier thing is that some trains go over tracks of different companies because they simply cooperate for the benefit of the consumer. You mostly don’t need to know whose line it is ever. The niche exception is for tourists with a JR Pass.
If you’re trying to remember a station in Shinjuku that was confusing with paper tickets, maybe you somehow used the Seibu Line? It’s “Shinjuku” but effectively separate from JR and Metro and a bit different as a result - or at least was the last time I needed it.
I don’t know many who ride that line unless living out on it or wanting to take the less crowded way to ‘Baba tho.
Paper tickets are confusing but basically nobody uses them. I don’t think it’s true that you need to get separate tickets for separate train lines. You do need to adjust your ticket if you prepaid the wrong distance.
Unless you mean two entirely separate lines separated by different gates.