Before you make the BIOS change, you want to make the change in Windows. Otherwise, you system will likely not boot with the BIOS in AHCI mode and Windows in IDE mode.
The easiest way to make the change in Windows 7 is to do this:http://support.microsoft.com/kb/922976
Run the FixIt in that KB article.
Reboot, make the BIOS change (sorry I dont know the answer -- likely the former is for the SATA II ports, the latter for SATA III and there are just two different controllers), save changes & exit. Windows will come up, install a new driver, ask you to restart and after that restart you're good.