The flexpilot integration is via the WebDriver so the low level test code looks something like
driver.execute_script("return document.#{theIdOfTheFlashObjectElement}.fp_click({chain: \"#{theChainValueShownInSeleniumIDERecorder}\"});")
where
fp_click is one of the methods provided by flex-pilot when the flash application calls FPBootstrap.init
I'm working with Groovy/Java, but that's relevant to the usage of Selenium/WebDriver, not flex-pilot. Your WebDriver scripts need to include Javascript that executes on the browser to invoke flex-pilot.