It might confuse him at first, but if from here on out you are consistent, he will adapt. It's amazing how successful crate training can be because you are catering to the dogs natural instincts (keep the den clean).

Puppies can hold it a long time in the crates because they sleep a lot in there. Just make sure the crate is not so big that he can potty in one corner and sleep in the other. That would defeat the point.