There is something existent called "dual intent" as per CIC's official guideline. Most people thinking you cannot apply for both (temp residence like work / study permit as well as PR) are plain wrong and should research dual intent.
In simple words, CIC does not care whether you permanently live in Canada or not eventually. When applying for study permit, they just want to evaluate that IF YOU DO NOT GET PERMANENT status eventually, ARE YOU LIKELY TO OVERSTAY ILLEGALLY OR NOT. This can be shown by strong ties to home country (not just owning property / business is the only way, which most people do not have) but rather having a established life / job with a respectable income in the same profession is a good and most common factor.
That being said, when you apply for study permit, having a PR application in process or not, you would be evaluated at the same grounds as another person with only study permit application. I believe i have read this formally several times in CIC's official description and should show up when you google DUAL INTENT.
UPADTE: So in summary if there was any confusion - there is no harm in applying for both study permit and PR at the same time, period.