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the way I did it was install windows first, then use the Linux CD (preferably a live CD) to do the Linux installation. During the installation it will run a partition manager, and from there you can select the drive to use for the installation. It will create a bootloader (grub, lilo) on the 1st disk so it knows where to find the 2 different operating systems.

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Q: How do you have two OS with two internal hard drives one running Windows 2000 pro and the other running Linux Ubuntu?
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