many MB's do not display any drives on the raid card as it is initialized after the bios goes through post. some high end raid cards and high end bios will display boot drives on the cards in the bios but its not fairly common for most consumer line products.
So should I plug the 2nd hard drive into the PCI Card instead of the CDrom? Would I be loosing any transfer speed to that HD if plugged into the controller card? I have a 7400 rpm hard drive and I'd like to utilize that to it's full potential because I do a lot of audio recording.
put both HD's in the card if you want, but why does it matter you cant boot from CD? how often do you really need to do this? a usb drive is much easier to boot from for os installs, diags, or any other off line work. if you must use a cd rom you could swap the cable when you need to use it. if you do boot from a cd rom on a very frequent basis then make sure the cd rom and os drive are on the MB and the storage drive on the sata cord.
Thanks a lot for the response. I use live CD's every now and then, and just want to be able to boot from my windows 7 cd rom if need be. Does connecting to a PCI controller card lose data transfer speed as opposed to connecting directly to the motherboard?
no, in most cases it will be faster than the MB. more so if the controller card has onboard cache. i would recommend using a usb drive for the windows and live disk. ive used a 16GB usb drive multi boot for all my xp-7 and live/ubcd boot disks for about 4 years now. works great