When you install Compressor all the ProRes and related codecs are installed and should be available when you're using Media 100.
Yes, you can use Compressor, but let me back up and make sure I understand what you're doing. Are you talking about importing the Canon footage into Media 100? If so you don't have to convert it first; Media 100 will do that for you.
If you're talking about working with an exported Media 100 file, then I suggest exporting the file as "uncompressed" and then bringing it into your compression program, such as Compressor.
You might also consider Handbrake:
http://handbrake.fr/downloads.php
