How do I go about implementing perspective projection with a 3D to 2D environment?

[the+university_guy]

I understand to some extent what perspective projection is, how it relates to homogenous coordinates, and how to transform a 4x4 matrix to a 3x3 matrix. But, I don't see how I could create a matrix to represent an entire six-sided cube. Maybe multiple matrices?
Does each 4x4 matrix represent a dot or something?