I am confused about what trains (or train systems) I have to use to get from Bruges to Nijmegen. i assume I have to change trains somewhere but how do I obtain ticket information, timetables, and so forth? Thank you.
If you are going to Nijmegen to catch the ferry you can take the train to Amsterdam Centraal and get off there. A bus to the ferry dock leaves from in front of the hotel on the corner, across the canal. Go out the front of the train terminal, across the trolley tracks, across the canal bridge, up to the front of the big hotel, go inside and ask the the concierge when the bus leaves for Nijmegen, and go down the street a few doors for a meal and a beer. Or, wander around a bit. If you are going to Nijmegen for any other reason I can't help you.
There's a number of possible ways to link the two cities. From what I can see online, the easiest is probably to take a train to Antwerp, from there to Roosendaal and then change at Roosendaal for a train to Nijmegen. Here's the website you should use: http://www.b-europe.com/Travel?utm_source=belgianrail.be&utm_medium=referral%2B-%2Binternal&utm_campaign=2013_general
PS- When you see the options on the website I posted above, as long your trip doesn't involve the premium Thalys or Fyra services, there is no advantage to buying your tickets in advanced. Simply buy them at the station on your day of travel.