Actually the boxes aren't empty. I have stuck cardboard slits into each box in the front and back end in order to ensure each books protection. I started doing this 6 years ago, when I began to notice how weathered the comics in the front and back were becoming. Because of this, I no longer have this problem. It didn't take me very long to fill up the boxes. Like I said in a previous post I use this software called ComicBase. I bought the deluxe edition with came with a comic UPC scanner. It has almost every ISBN in the history of comics programed into it. Again the cool thing about this is it updates automatically every week when books are released. However my favorite feature is that it will even scan though poly-bags to read the bar-code. Pretty impressive... But you are right in a sense, doing all of this by hand would be a royal pain.
-MathMan