I highly reccomend that unless you are an experenced painter you do NOT paint your boxes. Spray paint, unless done properly and with lots of care usually looks tackey and out of place. If you must paint your boxes a good wood primer is a must with MDF or else count on doing about 30 coats to get a decent solid color.
I also advise agianst carpeting. If you want carpet learn on a crappy test box that you built. Practice makes perfect. Use the good carpet, though it may not seem like its worth it a carpet with no backing and lots of strech will make carpeting easier, and often will make it look better. Parts Express sells some decent carpet for like $3-$4 a linear yard. Also, use a good adheasive, ive heard no complaints about 3M spray adheasive.So if im not sapposed to carpet or paint what am i ever to do? well my reccomendation is truck bed liner. Duplicolor sells a semi-gloss black for like $8 a can and works GREAT. i reccomend that your prime the box, do one light coat, one normal coat, and then, another normal coat if there are a few thin spots, then a mist to add texture. The stuf will cover any mistakes you made (well most) and 2-3 cans will do almost any enclosure you can throw at them. Also it protects the box from abuse and stiffens the wood even more.