It is automatic, I sent my OWP with my PR application, didn't do anything since the pilot was announced, and voila, I find a lovely brown envelope waiting for me in my post box. I am January 2014 applicant, got mine four days ago.
Tonyhomedad, if you have an AOR then they must have noted down what you included in your application package. And assuming that you paid the OWP straight up its probably in the system too.
My guess is the employer wouldn't care that your OWP is conditional; from what I remember they only ask for your sin number which doesn't say anything about your status. The only thing that gives it away is the expiry date but a lot of people got their permit that's good for two years which is no different than other types of work permit? Haven't gotten hired yet so I could be wrong though