I think the simplest solution would be to have the project and media files on an external/portable hard drive, as long as it’s 7200 rpm, not a 5400 rpm bus powered drive.
The main reason being, you wouldn’t have to reconnect the media constantly. as far as the project is concerned it’s always in the same place, on the specified drive.
Make sure you use the Canon E1 plugin and transcode your 5d footage in your project when you’re importing it. it works like a charm and keeps everything in apple’s efficient pro res 422 codec.