After that, alignment will be the trickiest part. After everything is set up, however, you should be able to do many boxes pretty quickly and accurately. I haven't actually tried this myself, but I think it should work. They will eventually rub off otherwise. Get some nice, clear spray paint.
Acrylic paint is nice.
Spray the entire outside of the box. This is mostly to protect all of your labels, the most vulnerable and important part of your chassis. Once you have done this, your chassis should be ready to go.