Even though my German is slowly (and painfully!) improving, I still don't enjoy navigating many of the public transportation websites for information about connections. My translation skills are weak and I have found that the English versions of the sites leave a lot out.
I have a really lazy solution: I usually figure out my trips using Google Maps. Under Get Directions, I click on the "By Public transit" image and type in my beginning and end points. It's great; I get the times, names and numbers of the buses/trains, and about how long it will take to arrive. I can choose timetables based on when I want to leave or arrive. Even better yet, the results are all in English!
Many readers might already know about this. It's a helpful hint to take a lot of the work out of finding directions, especially on public transportation.