ok you can but what i would do is unplug the master, just in case you reformat the wrong one,
and leave the slave in there, boot from the cd and install windows as normal.
then switch it back to slave and then plug the master back in, as normal.
and if you want to change the names of the os's (as it gets a bit confusing when given the os choice menu,) send me a message and ill detail it through with you