I have been playing around with lots of ways to do decals and have decided what works best for me is the Alps printer and CorelDraw.
The ink from the Alps is waterproof and the decals come out just perfect. If you get real good paper, the edges vanish and the whole thing looks just like paint! The best part about the Alps is that it will print white so you can use clear decal paper.

If you use an ink jet printer, buy some decal film from micro-scale. It comes in a 1 oz bottle and you can apply it with a foam brush after the decal sheet dries after coming out of the printer. You will need this to waterproof the decals before you can put them on the model.
Good luck, it is a lot of fun to do!!
Hans