If your BIOS is not seeing the CD, you've got problems other than no boot disk. Here's what you need to do (unless, of course you've already fixed it)...
Open the case. How many IDE devices do you have? If it's only 2 (CD and hard drive), then plug the CD into IDE2 and the hard drive into IDE2; 1 or 2 is probably marked next to the 2 IDE ports on the mobo. If not, look in the mobo manual. It will tell you which is which. Be sure the HD is plugged into IDE1!
If you have more than 2 IDE devices, you need to set the hard drive to "master" and the CD to "slave". At this point, you MUST hum "Master and Servant" by Depeche Mode. Otherwise it won't work. It's best if the song stays stuck in your head all day long.
To set them, check the docs that came with the hardware. It may be stamped on the drive, so check there, too. The jumper is the little plastic looking thingy that plugs over a set of metal pins on the back of the device.
Once this is done, start you computer into BIOS, and set it to autodetect all IDE devices.
Hopefully that will work.