Hi Mark,
First of all, the reason you are not using the screen setup on the EyeX Settings panel is because you want to use your EyeX Controller without a computer monitor, right? (As stated in this topic: http://developer.tobii.com/community/forums/topic/calibration-without-a-screen/)
To be able to set the active display area I gather you have downloaded the Tobii Gaze SDK and found your way to the tools folder and displayareacalc.html. The diagram you are referring to is the one in step 3.
To understand the diagram, please start by taking a look at the diagram of step 2. The colors in the two diagrams are corresponding: the blue color represents the screen area of the monitor, the light gray color represents the monitor frame, and the dark gray color represents the eye tracker.
When attached to a monitor the eye tracker is placed just below the screen area and slightly tilted upwards so the illuminators and camera are directed towards the eyes of the person in front of the monitor. The depth offset is the distance from the top edge of the front side of the eye tracker to the monitor screen surface (perpendicular to the screen surface).
The tilt angle is given by the geometry of the housing and the mounting area of the specific eye tracker and has to be specified in step 4. The default values that can be loaded using the buttons assumes the mounting angle that would result from mounting the eye tracker on a monitor frame with a surface parallell to the screen surface.
I hope this clarifies what the diagrams mean and what you need to measure and calculate for the non-screen case.