The size of the animation lay-up, by contrast, depends on the user's computer -- it will be chosen to fill the screen and use as much resolution as the user can afford (or as the user selects for performance reasons). Thus, pixel-based systems do not work.
After reviewing this with my favorite user, I decided to adopt a system in which the width of the Lay-Up is always 100 units (you can think of this as a percentage, for example). The height will vary, depending on the aspect ratio of the user's screen, but will be based on having square pixels (i.e. height and width are at the same coordinate scale). This does not mean that you are limited to 100 positions horizontally -- coordinates are floating point and can be defined as finely as you want (within the limits of the floating point datatype on the target computer, of course).
As with the pixel and SVG coordinate systems in AutoManga, the system follows ``traditional cartesian coordinates'' so that the lower left corner is (0.0, 0.0) and the upper right is (100.0, H), where H is determined by the aspect ratio of the screen.