If you want the 80gig master (which makes sense to me from what you are describing), keep it switched on master via the jumpers on the back. Make sure the other one is set ot slave.
Before you begin to look for it in windows, check the BIOS to see if it is recognized.
POST option
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When the computer boots up, it will display some information about the computer. If when you boot up, you see a spash screen logo (perhaps of the MB manufacturer) then hit TAB to view what is actually happening with the computer. Here it should say something like:
Primary IDE CH1: blah blah THIS IS YOUR 80GIG blah
Secondary IDE CH1: THIS IS THE ONE NOT BEING RECOGNIZED IN WINDOWS
Primary IDE CH2: And cd/dvd drives you have
Secondary IDE CH2: And cd/dvd drives you have
If you only have the 80gig recognized, and your CD drives. Then they are probable not plugged in correctly to the IDE cable, or they are not recieving power.
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If the text from "POST option" does not reveal a result, or you are unable to get to the screen I am describing, try this step:
When the computer boots up. You need to enter a key to get into the CMOS settings, or Bios, it could be labeled a couple things. To do this, it could be DEL, F2, or a couple of other keys. Since you recently bought the motherboard, use the manual that you haven't thrown away... to find out what key gets you into the BIOS.
After you are in, the General, or Main section will display a list of drives, this will look the same as I posted in the POST option with the IDE PRIM/SEC Channels. Here you need to see if both the 80gig and the other HD are recognized. If not, like above, they may not be properly conencted.
Post your results to this before I add more advice.