here is how I installed windows after linux in a second hdd. I use grub as bootloader. first I swapped cables where second would show up as first drive just long enough to install windows then revert it back afterward(I think some bios's can do this) now I booted into linux and edited the grub.conf like so.
map (hd0) (hd1)
map (hd1) (hd0)
Purpose is to trick windows into thinking it's on first drive