Copying Windows does nothing regarding the MBR. Two separate things.
Boot the Windows CD and when prompted, press R to get into the Recovery Console. Once at the command prompt, type FIXMBR. Reboot and you should now be able to get into Windows.
When installing Linux, you are asked where you wish the bootloader (GRUB or LILO) to be installed. Depending on your system, your first hard drive will be listed as hda or sda, the second drive being hdb or sdb.
IF you have the ability to set which drive to boot to via the BIOS, I would suggest writing LILO or GRUB to the second hard drive that contains the Linux installation, thereby leaving your Windows hard drive completely alone. Then all you need to do is use the function key that allows you to select which drive to boot to, then select the appropriate drive (Windows or Linux).