But you’ve worked in FCP before, correct?
As fas as codecs, you’ll need to do some tests to find the best image quality vs. disk space solution. You might want to consider DVCPRO HD if you can afford the room (it’ll look great). Apple also offers some Offline RT HD codecs which are fine. You want to stay in these HD codecs if possible to make the online easier. Otherwise I would edit in DV at 24fps. . . (this does present some technical issues you have to be on top of)
As far as protocol, it’s not much different than doing a :30 spot. I prefer to log and digitize sets of takes (scene 204, takes 1-7…. scene 204A takes 1-5, etc….) and then either use markers or create timelines of just that scene will all the fat taken out. These things ultimately depend on the editor, so you should ask. Even AVID people have different approaches when there is so much media to be organized, and ways they like to keep track of hero takes, etc…
Also, just like in AVID, I recommend cutting the film in chunks of 15-20 minutes. It keeps navigation of the timeline simple, and in FCP 4.5 the longer the timeline gets, the slower the box got.