Hi There

An MP3 file is always an MP3 file and can be played by any applications package that you have on your machine. To deal with the present situation, go to iTunes and pull down the Add To Library menu option. Now just add the new files to iTunes. Slow going, but the global alternative results in massive duplications to be weeded out.

For the future, go to iTunes Preferences and make sure that you have checked iTunes as the default format for downloads from the internet. Whenever you are downloading upgrades of any software which can affect music on your machine, it is always a good idea to quickly reinforce this iTunes default setting (Quicktime is always lurking and tries to sneak in when you're not watching).