Looks like I'll be doing some cutting after all. The GBA manuals are a tad too long to fit either way in the box. But if I put them vertically in there I can cut the little lip off the top of the manual slot and they'll fit nicely. I've also found that I'm going to want to find loose manuals for the games I don't have them for...
Yeah, if you don't use a laser jet you might as well print it in black and white.