Ok first make sure the sata drive is plugged into the #1 sata port so that will be seen as the first sata master even while this is for the post screen benefit mainly since you can install Windows even if the drive is on the last port when it is the only sata installed.
Recheck all cables especially the ide to verify which cable is on the primary not secondary ide channel. Also look in the bios to see how the setting for the onboard sata controllers is set and make sure that's not set for RAID. You may want to see both optical drives on one ide cable to see how that goes as well.
With many boards seeing the boot device menu option for a one time boot from the floppy, hard drive, or optical drive you choose from one of the catagories you can set the boot order to hard drive for first and second if preferred disabling the rest. Once you use the one time boot session to boot up with the installation disk and all setup files are copied to the intended primary now seen as E the system reboots without a need to change the boot order for the next step of seeing the installation continue. That's a time saver as well as a "lazy man's" type of tip there!
Prior to simply seeing Windows reinstalled you may prefer to simply delete the E primary and see a new one created to replace it. That will see any clutter wiped and give Windows a brand new primary to go onto.
A totally fresh install to avoid anything lingering should see C not another drive letter with the new copy of Windows being a stand alone installation on the sata drive. The second partition should then be seen as D with the optical drives at first being shifted to E and F.
Later you go into the Disk Management tool and right click on first the second 480gb second partition to see that changed to G or H where you can then set the first optical to D and the second E. You can then change the 480gb to F if preferred once the optical drive letters are set the way you want them.