Hi,
I strongly recommend you to install Windows and Linux independently on separate disks. The trick is to make Windows believe that it is sitting on the master drive, while it indeed is on the slave :-). See http://www.bioxray.dk/~mok/dual-boot.html for a more detailed description!
Thanks for this suggestion! Indeed I will do just that, as I intent to fully phase out the Win installation once I get a Vmware copy and it all runs fine (for the time being I'll have to go for a dual boot system). This way once Windows goes out the door it should be very easy to fully reformat the drive as an additional Linus drive (or just leave Win. sitting there and use the drive as an additional FAT32 datastorage).
Cheers! Olafo