We should strictly follow the steps as mentioned in instructions:
http://www.cic.gc.ca/english/immigrate/provincial/apply-how.asp
And pay RPRF when requested as mentioned, not earlier, you are right.
Noor, my advise is for paper based.. RPRF by the way is refundable so we better pay for it during application (in checklist, we can pay). in reality, we apply to get the PR, why we delay the payment if we are looking forward to the permanent residency?.. unless we are not sure to get it (PR)..