Embedding a Flash animation (SWF) into a page in Freeway is very simple. Just draw an HTML item and either drag the SWF from a Finder window or go to File > Import. The Inspector palette will change to show that you have a Flash file selected and using the third pane of the palette (Output settings) you can choose how the Flash animation should be handled. There are options to loop the movie, autoplay and whether you want to use the Eolas workaround that stops visitors using Windows IE having to Ok a dialog when the page loads.
To embed a Flash video file (FLV), you will need to use the FLV Player action, as they work a bit differently than the SWF files do. You can access the FLV Player action by selecting Insert > Action Item > FLV Player, or by clicking Actions on the Tool panel and selecting it from there. You can then choose settings for the video in the Actions palette.