1. Make sure you have latest MacOS (10.5.6 or highter), Quicktime (7.6 or higher), and FCP (6.0.5 or higher). And Intel-based Mac (2.8 Ghz recommended). You may still get some stutter during playback with multiple layers of video, audio, and transitions/filters. But output will be OK.
2. Make a Canon 5D Mark II pre-set:

Select Audio/Video Settings.

Select Sequence Presets. Select this one to duplicate and modify: DV NTSC 48 kHz.

Pull down Aspect Ratio and select HDTV 1080 i (16:9). that is is really correct but 1080p is not a choice but you will not convert to interlaced anyway.
Change Pixel Aspect Ratio to SQUARE. Do NOT check Anamorphic 16:9
Select Field Dominance Upper(Odd)
Editing Time base: select 30
Timecode Path: 30 Non-Drop Frame
Compressor: H.264
Audio Settings: Rate: 44 kHz, Depth: 16-bit, Config: Cannel Grouped

Under SUMMARY tab in Audio/Video Settings:
(make sure Sequence Preset shows name of the one you just made)
Capture Preset: Generic Capture Template
Device Control: Non-controllable device
Video Playback: none
Audio Playback: default
Click Create Easy Setup (put in your Mark II name) and click Create
Enable verification tab: checked

Now when you begin a new project, go to Easy Setup and pull down your newly-created Mark II preset.
Done! Now you can go ahead and import your movie clips directly from 5D mark II