Installing Controler Card Settings

I installed a 160GB Hard drive which came with a PCI Controler card and data cable, which I installed IAW the instructions. My CDROM did not work on the secondary controler card slot. So I connected it to the mother board secondary slot and it works but the computer needs the OS disk to start. Do I need to disable both IDE slots on the mother board so the computer will boot from the PCI controler card or what? Any help out there? Please!!