A lot depends on how often you'll use the keyboard tray. I use mine a lot so it doesn't have a cover over it, it isn't hidden, etc. Actually, it's used enough that I opted for the $16 heavy-duty keyboard tray that's capable of holding up to 50 pounds.
If you rarely use it then I've seen people simply lay a mini keyboard inside the control panel. If you have an mouse/trackball hack then that's obviously the mouse.
If you want a keyboard tray that is hidden you can use a couple hinges and another piece of wood to cover the opening made. The big issue would be that the hinged area would probably lay flat with the tray when opened and wouldn't be capable of holding a lot of weight.
If you never, ever use the keyboard but want the tray then you can just have a piece of wood that you can pull off. It'd sit flush with probably the bottom of the control panel, the top of the front panel, and the sides and would have a knob or something to that effect to pull it off. On the downside, with the tray open there will be a piece of wood just laying on the ground somewhere.
Hope some of this helps.