We've had great success with Nature's Miracle. It's enzyme based, there are different versions/different brands of the same stuff, but it's excellent.
Follow the directions, it will take any bodily fluid out of fabric/carpet (I think we've had to get out most of them).
With children and pets we buy it by the gallon and keep a spray bottle upstairs and downstairs.
*not that you asked, but crate train the puppy.
he should always be within your line of sight until he's trained--this cuts down on accidents of all sorts.