Assuming the PC software operates like the on-remote software, you will be able to edit the entire screen except for the top title bar/clock and the very bottom.

Your use of "discrete codes" is a bit strange... you see, it's not discrete codes you're after, it's some way of entering specific IR codes from over the net. The Cinema 7's database is much larger than they themselves use, so it has the capability to use "advanced" codes. However if the Cinema 7 doesn't have what you need built-in -- either completely or via advanced codes (which can be often) -- there's nothing you can do except learn.

The Pronto allows you to enter in IR codes based on a specific hex format. What a few companies already have done is include Pronto -> their format converters in their software, since that format seems to be so popular already... the TheaterTouch has one, and I believe Xantech also has one. Since the format is so well understood, I hope URC will either have one or include one soon.