I recommend setting both hdds to CS (cable select). This will simplify the whole thing.
Start up the PC and go into BIOS setup. Go into standard BIOS settings and see if both hdds are detected by the system and check their respective port position (primary/secondary, master/slave).
Next go to advanced BIOS setup and set the boot sequence. For example you can set the 1st boot device as CD-ROM, then the 2nd boot device as the hard drive of your OS and etc. For most newer motherboard you can set any hard drive as boot drive even it is connected on the slave IDE port.