asd, you should receive full instruction about paying the Right of Permanent Residence Fee in the email from Visa Office, after the Visa Office receive your medical exam results. I think that the payment method could vary from one Visa Office to another, in my case I can only pay at a specific Bank.
If you didn't receive yet the email from the Visa Office requesting your passports for visa, you could check your Visa Office website at the cic.gc.ca/english/information/offices/missions.asp . On the Visa Office website you should find a webpage with details about payment procedure.