The installation instruction has already been given in here http://drupal.org/node/303203 .

Now if you create a bat file in sites/all/libraries/flowplayer3/Rename.bat

where the Rename.bat has following contents;

ren flowplayer-3* flowplayer-3.x.x.swf
ren flowplayer.rtmp-3* flowplayer.rtmp-3.x.x.swf
ren flowplayer.audio-3* flowplayer.audio-3.x.x.swf

Then you can conveniently rename the respective player files for compatibility with drupal, just by running that batch file.