There are two types of animations that FS supports- the default (prop rotation, basic control surface deflection, tire rotation) and key-frame animation.
With default rotation, the animation of the part depends on the part name, part axis location/orientation, and, in some cases, an entry in the aircraft.cfg file to determine the extents of the animation/deflection.
For example - a rudder part must be named "rudder" (if you have a twin rudder, one can be named "rudder" and the other "rudder.1") . You model the part and move the part axis to the correct hinge line.
Your aircraft.cfg file will have a line indicating the rudder deflection angle, say 11 degrees to the right and left of the vertical hinge.
That's all you need.
In a key frame animated part you control the animation completely. You still have to name the part correctly. This is how you can have such things as fowler flaps, landing gear extension and retraction, special animations to control surfaces.
For detailed descriptions of the correct part names (tags) for both the default and key-frame animations, and the entries to be made in the aircraft.cfg files, check out the proper Flight Simulator SDK documents:
http://zone.msn.com/flightsim/FS02DevDeskSDK00.aspYou want to read and be very familiar with the MakeMDL and Aircraft Container SDKs.