To setup Affiliate, go to Preferences, and click Site Settings.
Click Affiliates tab
Default Affiliate Percent – the percentage the affiliates get.
Payout Window – the length of the inbound links, can be changed to weekly, monthly or forever.
Award Payment to – the affiliate who will get the payment for successful order from a customer.
Payment Methods Offered – your option from Paypal or Check or both
Show Affiliate Link Box in Sidebar – when turned on, you should also setup in the Layouts under Website Design & Content the Affiliates box and how you want it to be seen in each page.