I do it by trial and error. I have max opened on one window with the .geometry file loaded and the sceneEdit window opened with the character placed near a door or something else that makes it easy to compare relative sizes. I keep making adjustments to the size of the .geometry file and saving it to see how it looks in the game.
So the character size is fixed and I make sure the .geometry adapts to that.
But I have to use this weird method because I use maya to build the scenes, and then I just export the camera and some basic walkzones to max and that usually screws up my scaling. If you use max all the way just make sure you pay attention to the scale of things while making it. I find it's just easier and less time consuming to just adjust the .geometry little by little than worry about all that scaling during the creation.
Yes, I'm lazy...