Waterslides are a pain in the arse with a inkjet printer and are only really an option with a laser. With inkjet you let it dry then flash over it a couple of times with lacquer. Then apply. Fiddly, very fiddly.
Have a look at frequency central's OHP stylie way of doing it detailed on BYOC, which is cheap and cheerful and gets excellent results.
I do it differently still. I use adhesive transparent 'paper' from Crafty Computer Paper. It's easier to apply than waterslides once you have the technique down. Essentially print, apply, then press down to make the adhesive spread. This is the only real awkward bit in that you need to use the backing paper (so as not to damage the print) over the top of the decal, then rub hord on top of that with your thumb. Whilst keeping the backing solidly in place. It's easier than it sounds... After that, just lots of lacquer over the top and you're done. I drill the holes after the first couple of coats then apply the rest of the coats after that. Well, when I say I, I mean marauder, I'm ludicrously bad at spraying. If you're painting the box first it helps to wet flat it between coats. If like me you prefer the naked finish, just get the top of it as flat as you possibly can before you start.
Edited to add: The white adhesive decals give an excellent finish but have WAY stronger adhesive than the clear. They're really not easy to do at all. I try to avoid those when I can.
