Some values are read by FS2002 directly from the *.air file, but the corresponding values in the aircraft.cfg file will override the *.air file values.  So, if you adjust the gear lengths, etc, in the cfg file, these values will override whatever you had in the air file.

What some folks will also do is set the air file values, and not inlcude the corresponding values in the aircraft.cfg section, and let the FS2002 read and update the aircraft.cfg.   As an example, download an FS2000 model - that's not been "run though" in FS2002.  Make a copy of the aircraft.cfg file (you won't have a [contact.points] section, for example).  Open it in FS2002, and then go back and look at the aircraft.cfg file.