I don't have any problem with the control key position, I just swap it with caps lock.

The real pain for me is the meta key mapping. If I'm using Carbon Emacs I use one mapping, if I'm using emacs in a terminal I have to switch to another mapping. Things work a little differently with my external keyboard v.s. the built in one. I find the whole thing really irritating, almost enough to make me switch back to Linux on my laptop.

Anyway, I use http://doublecommand.sourceforge.net/ to map keys that aren't handled by the limited built-in mapping choices.