You will need to add something like the FLVPlayback added to the source flv. When you republish the flash it will have playback controls on.
Or you could program your own control in using stop()
and start()
etc.
If you wanted to use a jQuery approach you can use jQuery SWFObject. This will embed the swf and give you a options to control some aspects of the swf. Although additional changes to the source maybe required.
You can find examples here http://jquery.thewikies.com/swfobject/examples