I phoned CIC in advance about my travels and the officer I spoke to told me that travelling is always a risk and entry can always be denied by the border officer. She also told me not to travel to my home country, because my PCC would become void.
I guess there are people who successfully traveled home and back, but I didn't want to take the risk. Now I feel like I am so close to PR that I don't want to take any risks anymore since the OWP is linked to PR application. My previous IEC visa was not linked to PR.
You can read more about travelling while in process here: here:
http://www.cic.gc.ca/english/helpcentre/answer.asp?qnum=248&top=28
In regards to your passport question, isn't there a section about citizenship in the PR application forms? I think you are supposed to indicate all your citizenship documents there. I am not sure though.