If you choose CS for jumper settings, the absence of a Slave on the middle connector of the ribbon cable is NOT supposed to be any problem at all. If you just want to be sure, set its jumpers to Master instead.
Look closely at the way your BIOS names things. Some use terms like IDE Master 3 etc for actual SATA ports (clue: there is no IDE Slave 3 because there is no Slave in SATA). So it MIGHT cause you confusion in the Boot Priority screens.
In Boot priority it is more common to set the first device as the optical drive. Setting it second AFTER the HDD will mean you cannot boot from the optical drive at all unless your HDD fails. But putting the optical first, and then NOT putting a bootable disk in it, will allow that drive to be tried first and fail, which then causes the system to go on to the second boot device, your SATA drive. As you work on these, watch out for its default actions. Often if you change one, it will fill in other options on other lines for you. That MIGHT end up putting your old drive on the IDE port into the sequence, and you do NOT want it in there at all.
I just looked through the manual for the ASRock P55 Deluxe board (not sure if that's yours). On p. 66 it covers configuration of drives, and I see a potential source of confusion. The first line called "SATA II Operation Mode" and the default choices is "IDE". This does NOT Enable the IDE port. Is sets the SATA ports 1-4 to IDE Emulation Mode so that Windows thinks it is dealing with an older plain IDE device, rather than a SATA or AHCI device. This is mainly for use with Win XP, probably not necessary with Vista or Win 7. Lower on the screen are the lines for details of what device really is on each SATA port. Still in the upper part of the screen, though, is a line called "Onboard eSATA and IDE" which must be Enabled to use either eSATA, IDE, or both. If Enabled, then you can configure the eSATA port mode on the next line (similar to the modes on SATA 1-4). Now, near the bottom of the screen is the line that shows what eSATA device, if any, is connected. Then the last two lines show you details of the IDE devices connected, and THIS is where you must make sure your IDE Master device (your old drive) shows up and is configured properly.