I have done this in Quark, and also in Illustrator.
Be aware that there are a lot of technical issues in making boxes having to do with folding radiuses, flaps, bleeds, and die tolerances. Having a template from your printer saves you from having to learn all of it at once.
Being able to work in layers (as in Illustrator, or in Quark with certain Xtensions) is a great convenience, since you aren't bumping into construction and die lines all the time.
Layouts for (larger) boxes can be sprawling, and the larger pasteboard that Illustrator offers can be useful. The alignment and pathfinder tools are also a little more useful, though Quark is catching up a little here.
Good luck, and remember that a phone call to your printer to setttle questions is a lot cheaper than rerunning a job¡