Well, it involves changing things in both, but mainly in Windows. It is a complicated process, but it can be done in 2 ways: Fresh re-install of Windows, or modify current install. If you do the latter, you may experience more problems.
You have to update the driver for ACPI Compliant System in Device Manager, change it to Standard PC. When you reboot, it will re-detect all hardware again, and you may lose some power management features, such as being able to power off your computer automatically w/o pushing the button.
I only suggest doing this if you have serious problems or lockups with IRQ sharing and your devices. I currently have 5 devices sharing IRQ7, which I think is bad, but I do not get any major issues with this configuration.