Yes, it will work with all the checkout options of the WP-eCommerce Plugin after you complete the following integration (example, PayPal, Google Checkout etc).
Please follow the steps outlined below to integration WP Affiliate Platform with WP-eCommerce plugin:
Integration Steps for WP eCommerce Plugin
Step 1) Make sure you are using WP eCommerce Plugin.
Step 2) Simply install and activate the WP Affiliate Platform Plugin and it will start to track any affiliate sale that you make via the WP-eCommerce plugin.
Now, after a sale when your customers land on the “Thank You/Transaction Result” page the plugin will award the commission to the appropriate referrer.
Remember to test it after you do the integration to make sure everything is working fine before you go live.