They are one of two box designs, either they are both ported and the one with the square hole is using an internal "tunnel" as it's port, or it's a bass reflex box which is a whole different story.
Both box types take specific planning and design to work with the specific sub(s) you put in them, so don't think if you cut a hole in your box you'll have a ported enclosure. Not that you're planning on doing that, but I've seen it happen. //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif
Here's a good article to read, it will give you a good foundation on enclosure types.