Without seeing your site or knowing what it does, that’s a tough question to answer exactly. However, I can give you some insight on how we sometimes use the FlashVideo module.

For sites where things need to be a little more tricky than FlashVideo is by default, we usually end up using FlashVideo more for its ffmpeg interface than anything (Media Mover with the ffmpeg wrapper may ultimately turn out to be a better solution, but I have encountered bugs getting it to work locally on windows — but I digress). I will say that lately I don’t really ever use the [video] tag.

So once we have the videos converting (and in your case, storing them in their respective per-user folders, which is a whole other can of worms), I suggest just using some relatively simple php to inject the url of your node’s attached FLV video into the player html code. Then you can easily specify a path to the player relative to your drupal installation. That way the video player files don’t need to be duplicated. For example:

<?php
foreach ($node->files as $file) {
     $filepath="/".$file->filepath;
     $file_extension = substr($filepath, -3, 3);
     if ($file_extension == "flv") {
          $video_url="&file=".$filepath;
     }
}
?>
<script type=’text/javascript’ src=’/files/swfobject.js’></script>
<div id=’player’>Loading Video Player</div>

<script type=’text/javascript’>
var s1 = new SWFObject(’/files/player.swf’,'player’,'400′,’300′,’9′);
s1.addParam(’allowfullscreen’,'true’);
s1.addParam(’allowscriptaccess’,'always’);
s1.addParam(’wmode’,'opaque’);
s1.addParam(’flashvars’,'<?php print $video_url; ?>’);
s1.write(’player’);
</script>

Hopefully this helps.