The way I designed my cabinet was to mock up a control panel, and then adjust it for perfect height.
To do this I just built a three-piece control panel (top, and two legs), and then put it on my breakfast bar, and adjusted it with magazines under the legs until I found the perfect height (38" for me).
Once I knew that, and the optimal angle for the CP, I designed around that.
At that point, I built what was basically a rolling table to hold the monitor/CP, and then designed the skin of the cabinet around that.
That method worked really well for me, but I had some involutary indecisions while designing.
My wife didn't want me to decase the brand-new 21" monitor that I bought, so I had to make the cab larger than was absolutely necessary.
As far as the monitor/TV goes, you should definitely decide on what you want, and how you want it (in the case, or decased) before you begin overall design plans.
If you don't know what you want before you begin design, you are going to have to design generically, so that you can fit whatever you get later.
If you know beforehand, you can design specifically, and end up with a much better result.