You may actually have no problem beyond very confusing words your mobo uses.
The matter of "setting" a SATA HDD to IDE or SATA or AHCI is part of a work-around from the early days of SATA and Windows XP. XP never had a built-in device driver for AHCI devices so technically you had to install a driver for them from a floppy disk during the initial installation of Win XP. To avoid that hurdle, many mobo BIOS's offered an option to set the manner in which it used the SATA HDD. You could tell it to use "IDE Emulation" which simply limited the SATA port to using only IDE capabilities, and made the OS believe that the device really was only a simple IDE drive that Win XP COULD use with its default IDE device driver. However, doing this did NOT make the SATA device an IDE unit, and the BIOS did not call it IDE for this reason.
On the other hand, many earlier mobos with both IDE and SATA ports on them used labels and words as if the SATA ports were just more IDE ports. They did this even though they were using the SATA devices properly as AHCI devices! So mobos like this might display that they had a Master (and maybe a Slave) drive on their Primary or Secondary IDE ports, plus more IDE devices on additional ports. But the last part there is wrong - the additional ports really are true SATA ports! The BIOS was simply using the wrong words to display info on the screen.
Even if you are using a Windows after XP - and beginning with Vista, Windows DID have built-in drivers to use SATA units properly as AHCI devices - and hence are NOT setting your SATA drives to "IDE Emulation" Mode, the BIOS may misinform you about the units attached to the SATA ports. If that is your situation, don't worry about it. It is not causing a problem, and you can't change it.