Usually Flex applications uses a regular HTML pages for authentication or by other support. When this is the case, FunFX alone is not able to get to the Flex part. In these situations you can use the excellent tool Watir.
To make Watir work together with FunFX you do the same setup as usually with FunFX, but you also require watir, and attaches Watir to the browser FunFX started. With the example below I use the the title of the page to make Watir understand what browser to choose.
When you have done this, both the FunFX instance and the Watir instance is able to control the browser. But one thing you should watch out for is that when FunFX enter the Flex application, it must set the flex object again, so either if you use FunFX to navigate to the Flex application, you can define the flex object in the goto statement. Or you can use the setFlexObject method.