I've been wanting to do that for a long time - but so far haven't had the time or energy to try. Are you sure you can't just move the My Documents folder from c: to d:? I think this is possible, at least in windows 7. The same for your desktop.
If it doesn't work directly, you could try to make shortcuts to it. If the shortcuts work, then you can go onto your other OS's c: and delete the My Documents and Desktop folders there and replace them with shortcuts to the appropriate folders on d:
I've never found any conclusive way to do this easily, but then I've never tried very hard
By the way - do you want the same programs on both, ie exactly the same copies with all the same settings etc? Because that could prove more difficult. There are user settings files stored deep within the c: directories which would be tedious to pick out one by one.
I really think you should ask this elsewhere as well as here, because great as this forum is for speccing rigs and fixing hardware glitches and many other things besides, it's not really software orientated and there may be other people elsewhere who are extremely good at this sort of thing.
EDIT: I checked the software RAID thing - it works in Windows 7 fairly easily via Disk Management (manage HDDs and partitions) --> Select Empty non-formatted drive and right click --> Select 'Create Mirror' --> and then add the other partition (I don't have enough free HDDs to check this last step, but I suspect that it should work without too much hassle)
However - it is questionable whether a software RAID would work if you had to set up two separate ones because you are dual-booting, and I would strongly suggest buying a £5 RAID card, if RoboCopy turns out to be rubbish.
And couldn't you write the script for that? In fact - if you get the GUI version, everything's represented by pull-down boxes and the like so you shouldn't have any trouble with it at all.
Gah - command line interfaces do not mix with the average Windows user