You can pay online for Family Class applications. Go to the
online payment site and agree to the disclaimer > under what services you need, click the Immigration link > under Where will you be sending your application, click Mississauga, ON (because all outland spousal PR applications go first to Mississauga) > confirm the location > under Permanent Residence, Family Class applications enter the number of each type of fee you're paying so that the calculator will give you a total - in other words: 1 sponsorship fee @ $75, 1 applicant fee @ $475, and $150 for each accompanying dependent (if applicable). You can also pay the $490 Right of Permanent Residence fee, or defer that until later on in the process.
Once you calculate your fees, you'll be asked to create a username and password type thing so that you can access the site later for a record of past payments. Then they take your payment info, and generate a receipt that you print out and include with your application.