Man, trying to figure stuff out on their web site gives me headaches.
I've found that just showing up at the station (esp. a day beforehand) to sort out timetables and fares made life easier. The people working the desks at each station were amazingly helpful, even printing out timetables for me, figuring out the quickest routes, cheapest fares, etc.
Granted, if you don't buy in advance, the fares can be pricey, but if you're going with a pass, then I don't think you have to worry too much.