While Final Cut Pro will edit the H.264 files created by the Canon 5D or 7D, it will be slow and probably not frame precise. A much better solution is either bringing the files in through Compressor or using the free Log & Transfer plug-in from Canon. It is important not to strip away the .THM files if you plan on using the the plug-in. In fact, the plug-in requires the DCIM folder to stay intact. I suggest you copy the card on to your drive and backup drive and simply use a naming system to change only the master folder name. The Hoodman RAW firewire card reader will help speed up the process, see side panel for link.
Once you have the original master folders safe, you can proceed to convert the files into the ProRes format of your choosing. Most think any of the ProRes versions above standard ProRes does not gain anything in quality.