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PRE does not have a 1080p option.
From the specifications (HD 1920 x 1080, MOV (Video: H.264, Sound: Linear PCM) you will need a "AVCHD Full HD 1080i 25" project setting.
I suggest you try with a small clip first to see how good the output is. Note that the Internet has many sob stories about using 5D video footage.
If you don't need to do too much with the file you could try QuickTime Pro - others post here saying that this is a great tool for .MOV files. I think you can also use QuickTime Pro to convert to a more PRE friendly format, perhaps other 'regulars' could comment.
Insanity is hereditary, you get it from your children
Thank you very much! Leif
This ARTICLE has a lot of links for DSLR footage. Some apply directly to PrE, but some are for PrPro exclusively. There are also several tutorials on working with DSLR footage in an NLE program. One was just updated, but the link is the same.
PS - last month's American Cinematographer had several articles on feature films, at least partially shot with the Cannon 5D's.