This helps. I was able to make the changes through the registry. Within SCCM 2012 I ended up having to do an active deployment where it applies the registry settings at each users log-on once. This allows each user to get the same preferences. I wasn't able to do so with the Adobe Customization Wizard as it's a HKCU setting and needs to be ran for each other. Unless there is a different way of doing this? For now, this is a solution that will work for my environment.
Thanks Sabian for the quick responses and assistance!