You can clear the CMOS by moving the jumper closest to the battery. The battery is the large silver cylindrical thing, about the size of a quarter. Move the jumper closest to it, one pin over. Then hit the power button on the front (nothing may happen, this is normal), then turn off the system (if it came on), and switch it back. The three prong cord sounds completely optional since it comes from the front. Probably for a light, fan, or the connections on the front.
The reason I ask the error is because if you jot down the specific error message/number, you can plug it into google and find SOME other person who had this issue, or something very similar. This is definitely a very rare problem that a system will not work with several HDDs, although the rest of the components seem to work fine when running an OS booted from CD.