Hey no worries man, introducing people to Japan is pretty fun because it's such a strange place (*´∀人)
Anyways, don't worry - you really won't stumble across a bad place unless you're actually looking for trouble, normally these places are at places where there is nothing interesting anyways, hehe
Aaand about the trains I'm not so sure what you mean here with "one time"
Here's a note, the trains and buses are always always always always on time by the second!!! This is freaking amazing, if the train comes at least 5 minutes late (which the chances are 1/10000, only happens after a small earthquake, usually) you can ask for a ticket from the people by the station explaining to your boss/teacher why you're late!! Once you're there, take a look at the clock at the airport and sync your clock so it's exactly the same by the second - then you will have the most accurate time across the world, haha! Word of warning, when you come back to NL, you will be so incredibly annoyed waiting for the bus or train once you're used to seeing the train or bus arrive by the second in Japan... When I came back here I got soooo frustrated if the bus wasn't there even 2 minutes after the scheduled time hehe (○´∀`○)
And Yamanote line is the 'loop line' which goes around most of the big places, probably the most handy if you're lost. I've only lived in Tokyo for a year or so so I don't know so much about the place as I know about Kanazawa..
Also heads up, you can't use the JR passes in the metro, so I suggest using the JR trains as much as possible, as the metro can be mad expensive..!