Not quite sure what exactly you are trying to do ... but lets say that your problem is you have embedded flash w/ video and you need iphone/itouch users to be able to access this video too ...
first thing you will want to do is to do a browser check for 'iPhone' or 'iPod'. You can do this in JS but I prefer to check server side.
JS would be
if((navigator.userAgent.match(/iPhone/i)) || (navigator.userAgent.match(/iPod/i)))
{ code for qt } else { code for flash }
PHP would be
if(eregi('iPhone', $_SERVER['HTTP_USER_AGENT']) || eregi('iPod', $_SERVER['HTTP_USER_AGENT']))
{ code for qt } else { code for flash }
Next you will want to export your video using quick time pro and the "Export for web command" this will compress all versions for the iphone and ipod touch and a poster screen for the end user to click on.