First of all I agree with europhile, you don't want to spend most of your time in a train. Another tip : go to Bruxelles, friendly people, great food and even better beer.
If you travel to Amsterdam and want to go to Berlin by train, there is no need for pre booking, unless you want to have a certain seat on a very fancy train; when you want to take the train you go to station and ask for a ticket to Berlin.Train services in Holland/Germany are a little more frequent than Ireland due to the number of people travelling by train.