Your machine has usually 2 channels for your attached storage, some mobos have more and you can always add on some with a controller card. Channel 0 contains 2 devices device 0 and device 1 while channel 2 also contains 2 devices being device 2 and device 3. You WILL have a HD on channel 0, but your CD/DVD drive can be on any of the other 3 channels. If you can without conflict set your CD/DVD drive onto channel 1 as a slave using device 2 to your primary HD as device 1 on channel 0 then that'll leave you with devices 2 and 3 free on your second channel for your 2 hard drives to use in array.
The pic I made below is for IDE setups, but the same goes for your SATA drives, except you don't have to set the drives as master/slave. I'm also assuming your primary HD is PATA not SATA and we all know your CD/DVD drive is PATA.