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What was the configuration before you changed it? Linux on one drive?
The first thing I would do is make sure it still works the way it was. Suppose that you are using drive 1, AKA /dev/hda, and the BIOS is set to make that the first drive. Installing another drive should not affect the booting of the first one. To be sure, however, check the bios to see what it sees when both are installed.
Next, you will need to modify the bootloader configuration on #1 to correctly point to the Linux install on the 2nd drive.