1.-First plug the external HDD to your mac, boot said mac.
2.-If you can see both the internal and the external HDDs in the finder try changing their names to "Internal" and "external" without the quotes. if you can only see the internal HDD take note of its name.
3.-go to system preferences and click on "startup disk"
4.-check that your internal hdd is selected as the startup disk tomake sure you are booting from the internal hdd
5.-quit system preferences
6.- launch disk utility
7.-if you are booting from the internal hdd, you should be able to select the external hdd and follow War's instructions to erase and format it.
8.- if you can't select it in disk utility there may be something wrong with the drive, also try using a different cable to hook it up.

good luck, hope this helps

Kisin