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I have the same question as igor8 asked. Really, logically speaking, bootloader should be installed in MBR in the first HD. Does it matter if I use the 2nd HD for Linux? or I have to install Linux in the first HD?
Just remember when dealing with windows. Windows must always be the primary. Weather its on the first partition or on the first hardrive. Windows does not like to be second best. As far as the bootloader. I would always overwrite the MBR of the windows partition/drive. why? because the windows bootloader sucks. And grub is so much more easier than dealing with the windows boot.ini file. So in both your cases, Have windows on HD1 and Linux on HD2 with the bootloader in the MBR of HD1. And to do yourself a big favor make a boot disk for your windows just in case.
Captain storm in your case i would use rawwritewin in windows to make a cdrom boot floppy for install. Just look on disk 1 for a dosutils folder and it should be in there. have a formattted floppy ready. and browse the images folder for cdrom.img thats it.