My advice is, if this is your first bimmer get a professional to do it. It'll take them less than half the time and they won't wreck anything. I just replaced (not personally -- I had it done at a car audio shop) my "Business CD" factory deck with a new high-end Alpine head unit -- and there were an awful lot of wires coming out of the back of that thing! The connected iPod sits in the glove box and all the iPod screen's functionality now works on the new deck. (This probably won't be the case if you get an Icelink or some such.)
If you DO decide to do it on your own, one key item is that to get enough room to manouver behind the dash, you have to pop out the center vents -- not an easy thing, especially if they've never been popped out before. Whatever you do, don't use a screwdriver. You'll wreck the plastic around it. Take off the trim around the deck and use your thumbs to pop the bottom of the vents out.
The other thing was the glove compartment has to be detached. Luckily, though, you won't have to do any drilling to get the wires for the iPod (which I'm guessing you're planning to store in the glove box).
Whatever you decide ... good luck and happy listening/driving!