If you are just playing straight video and don't need the capabilities of flash video, save yourself the trouble, and use the video tag and bypass flash.

If you do want to use flash video and serve html5 video, do yourself a favor and use swfObject to load the flash. And inside the div tag that the swfObject rewrites if the user has flash, place the video tag for html5 (serve both MP4, and webm). (you can get swfObject from google code). If they don't have flash (ie bowsers with no plugin and iOS etc), the flash will not be written in, and the video tags will work.

That will solve everything. If the user has flash, they'll see it. If they don't, they'll get the html5 video.

Seamless, and simple.