I know this thread has been dead for a month or so, but I viewed it and had to add something to it for any others that may come across it…
Eric is right as far as how you should have your sequence settings, but you should DEFINITELY TRANSCODE to a different codec. You can look this up or ask any person in the Canon 5D filmmaking forums (that has experience with a Canon 5DMKII workflow) and they will tell you the same.
Premiere Pro CS5 & FCP 7 (I assume FCP X too) can all edit your footage natively, but doing so excludes extra quality that is compressed that you could get from transcoding the footage. For Premiere Pro I would suggest something with an AVI container. For FCP use ProRes 422.
I use NeoScene which transcodes your 5DMKII footage to AVI or MOV depending on your OS. It changes the chroma-subsampling to 4:2:2 from 4:2:0, and moves you color bit-depth from 8 to 10 (4x the color information of 8-bit!). If you plan on doing professional color correction, this software is worth every penny!
Check out the 5DMKII footage done through NeoScene on YouTube, or where ever you can. I bought the codec and have used it for every project since. The amount of visual information that is “enabled” is just remarkable!
Also, unrelated to this issue, if you do own a 5DMKII or 7D, check out the technicolor cinestyle color profile, and the Magic Lantern Firmware (to boost your sound and bit rate quality).