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Your use-case is HDS or RTMP playback?
For RTMP VoD playback, refer http://help.adobe.com/en_US/flashmediaserver/devguide/WS0432746db30523c21e63e3d12eea2a8fc0 -8000.html. You can goto section "Configure the location of media files".
In case anyone is curious, it looks like the best thing to do is store videos on Amazon S3. You can then mount that as a drive onto your server, and stream videos from it. However, I'm using Windows, so that brings all kinds of extra hoops to jump through, and I have not figured it out yet.