Crates for dog training work well as long as he doesn't start to associate them with unpleasant experiences.
Things to consider: Uses of a crate, size of the crate, and house-breaking techniques.
Pleasant Place - Crates are great for dog training but they are not doghouses and should not be used as such. Though dogs are naturally inclined to feel safe and secure in a den-like environment, to keep them feeling this way about their crates, don't leave them alone in the crates over long periods of time. If you need to confine your un-housebroken puppy, then put the crate inside a room that is closed off with a dog gate. That way, she can go in and out of the crate as she pleases and she is unlikely to ever consider crates an unpleasant place to be.
Size It Right - Wire crates often come with a divider so that you can get one crate for the size your dog will be when full grown but until then you can still keep her confinement area small enough that she does not have room to "designate" a separate bathroom area from where she sleeps and eats. Plastic crates, however, may give your dog a more den-like feel and are generally more portable, with handles for easy carrying.
Letting You Know - Signs that your crated dog needs to eliminate are sniffling, circling the area, or acting restless. If you witness any of these signs, take your dog outside to eliminate immediately. If you want your dog to learn that the outdoors is really the only acceptable place to eliminate, when you can tell that your dog might need to go, don't just idly stand by and watch her go in her crate.