So, as I understand it, you should be using an SWF file (the player) to control and play the FLV files (the videos)?
That's the impression I get when Flash Video Studio spits out both of those files... When you run the SWF file (the player), it loads and plays the FLV file.
Am I on the right page? If so, would I use ImTOO FLV Converter to create FLV's for loading in my SWF player?