You'll want to use SATA native mode rather than IDE mode, for the main reason that faster data transfer rates can be achieved - http://www.computer-hardware-explain...ta-vs-ide.html
It's possible to enable AHCI / SATA Native Mode in Windows after already having installed the OS under IDE / Legacy / Compatibility mode. I've had to do this myself under Windows XP as well as Windows 7 a few times before.
For Windows XP, this process (in a nutshell) involves downloading the relevant SATA driver, manually updating the storage controller with the SATA driver (i.e. manually installing the SATA driver) in 'Device Manager', rebooting the PC and entering the BIOS settings to switch from IDE mode to SATA Native mode, and lastly booting into Windows to finalise the process - Windows should then automatically detect the SATA controler and install the SATA driver (one last reboot may be required if prompted).
For a step-by-step walkthrough (with screenshots) check out the following support article:
How to enable AHCI : Windows XP « Expertester
Windows Vista / 7
For Windows Vista or Windows 7, you can follow the same process. However, since from Windows Vista onwards there is native support for SATA in the OS (i.e. SATA drivers inbuilt into Windows Vista and Windows 7) you can simply boot into Windows under the current IDE mode, apply a registry tweak to enable SATA detection, reboot the PC and enter the BIOS to to switch from IDE mode to SATA Native mode, and lastly boot into Windows to finalise the process. This works for all, if not the majority of SATA controllers.
For instructions, check out the following support articles:
AHCI : Enable in Windows 7 / Vista - Windows 7 Forums
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Error message when you start a Windows 7 or Windows Vista-based computer after you change the SATA mode of the boot drive: "STOP 0x0000007B INACCESSABLE_BOOT_DEVICE"