It's all about placing the origin brush because that's where the model will appear based on it's own origin. In GtkRadiant you can see a models origin box. I've heard that with q3map2 you can link a model to a train and it will follow it, I haven't tried it myself.
As for the wobble effect you probably need to make a ROFF file. Don't ask me how but I think you need 3ds max. Take a look at the script for the skiff in Nar Shaddaa, if I remember correctly it moves around with code from a script.