Make the box so when you sit on it, you are an inch or 2 below parallel. That way, sometime in the future when you want to box-squat deep, below parallel, you are covered. For "normal use" you can put a 45 pound plate, or mats, or whatever on the box box to jack it up an inch or two.
Or you could build a couple 2 inch risers. Just 2x4's in a square, with a piece of half inch ply wood on top. If your box is 2" below parallel, one riser puts you right there. 2 risers lets you squat a little high for overload.
Then you can do deficit or blocks deadlifts and pulls on or off of your risers too.