I actually use both those methods. I was used to the "copy-paste" system with the old software I had, and I still use it a fair amount. It has the big advantage of being able to flip a selection sideways (left-to-right inversion) to break up patterns when you're filling in foliage or something. That was easier with the old software (maybe I just haven't found the way to do it easily with PdN; in the old program, as long as something that had been copied and pasted was selected it was considered as being on top of the picture until you shut off the selection, and "flip horizontally" just reversed it the same way putting it into a different layer and flipping the whole layer does it with PdN, with a few less manipulations to boot) but works wth PdN, too.
Still, I love the clone tool, and as long as you make sure you're aiming at the right layer (both for anchoring and for drawing), I really don't see how it's hard to use.