What I did was research some tried-and-true designs online to extract common ranges for "key" dimensions (such as total height of the cabinet, and height of the CP top surface). I fixed those in Sketchup, then started working in the other known quantities (such as dimensions of the monitor--screen width, screen height, and casing depth for CRT). I then figured out the approximate height of my eyes when I'm standing, and drew a line that tall in sketchup out in front of the cabinet, and drew another line from my "eye height" position down to the screen. Adjusting the view in sketchup to "gun sight" the second line, I could get an idea of whether the screen angle was good or not.
Once you have all those critical items fixed (or at least, within some bounds) you can just go nuts and build a box around it. I had all kinds of crazy ideas but ultimately I ended up going for a basic "archetypal arcade cabinet" look because I wanted to make sure that I didn't design in features that would be too difficult to achieve with my rather novice woodworking skills. There is nothing radically original or jaw-dropping about my cabinet design but I do take pride in the fact that I at least designed the thing from the ground up and now I have a one-of-a-kind.