A GPO that is linked to a specific OU should process after a GPO that is linked at the root of the domain, and those settings in the OU-linked GPO should win out in the end, correct? This is the scenario we are proving out today. You probably remember the GPO I created previously that set my desktop wallpaper to the color blue with a large number 1 in the center. This policy is linked at the root of my domain, as you can see in the following screenshot, and as you can also see, it is successfully applying to the LAPTOP1 workstation where I am currently logged in:

Now I am going to create a second GPO that sets the desktop wallpaper to the color orange, with a number 2 in the center of the screen. This wallpaper setting is in direct conflict with the wallpaper setting in my old GPO, and so if both GPOs apply to a workstation, only one of them is going to win at the end of the Group Policy processing cycle.

Remember that simply creating this new GPO will do nothing until we link it to a location. I have created my new Set Desktop Wallpaper to Orange 2 GPO and, as seen in the following screenshot, I have linked this new GPO to the Accounting OU. This OU happens to be the place where my LAPTOP1 workstation resides:

When I reboot LAPTOP1 and log in, Group Policy processes both settings. It first applies the Set Desktop Wallpaper to Blue 1 GPO because that GPO is linked to the root of the domain. It then proceeds to apply the settings from the Set Desktop Wallpaper to Orange 2 GPO that is linked to the Accounting OU, and when the login process is finished, you can see that the wallpaper configured on my client is orange with the number 2:

This example is nothing earth-shattering, but is definitive proof that I'm not making this stuff up, and that conflicting settings will overwrite each other depending on the GPO processing hierarchy.