I am having exact same trouble as you. The closest thing to documentation of the commands is a blog post that shows a couple of examples of what the desfire communication looks like.
http://ridrix.wordpress.com/2009/09/19/mifare-desfire-communication-example/`
But there is a library that can help you with putting desfire commands together:
http://code.google.com/p/nfc-tools/wiki/libfreefare
Edit: It turns out that you can't get the documentation freely. You need to sign an NDA and then buy it.