You can also use the media manager in the latest version of Desktop manager. Simply browse to the file, using the media manager and drag it over to your BB. Pretty simple.
Yes the media manager is the best bet for transferring ringtones that are located on the device and not on an external storage card. Personally I have found that there is no detrimental effect of having the ringtone stored on the SD card VS the actual device but I would be curious to see if anybody has tested this out fully.
Its a shame it doesn't seem possible to save .wav file attachments from emails. This would be the easiest way. I attempted using the media manager from the latest desktop manager and it just did not work.
Well, it was described above other options to do what you need. You didn't answer my question, so it difficult to determine why your Media Manager won't work.