For Cisco CallManager 3.3.3, drop the files into C:\Program Files\Cisco\MOH\DropMOHAudioSourceFilesHere.
For Cisco CallManager 3.2, drop the files into C:\Cisco\DropMOHAudioSourceFilesHere.
After placing the files in these directories, they should get converted and be available to Cisco CallManager.
This is a CPU-intensive process, so it should not be done on a server that is actively processing calls because it causes the CPU usage to spike. Go to Service Media Resource > Music On Hold Audio Source from the Cisco CallManager Admin page, and add the new file as a Music on Hold (MOH) Audio Source.