There are a few considerations or changes when using the newly separated from the core AD Provider.
Primarily the AD Provider has been moved to DesktopModules/AuthenticationServices/ActiveDirectory and a new .dll is used (DotNetNuke.Authentication.ActiveDirectory.dll instead of DotNetNuke.Authentication.ADSI.dll). This results in two major changes, one in the web.config and one in IIS permissions.
I don't know if this will show up properly in the blog but no longer is < add name="Authentication" type="DotNetNuke.HttpModules.AuthenticationModule, DotNetNuke.HttpModules.Authentication" /> used and has been replaced by <add name="Authentication" type="DotNetNuke.Authentication.ActiveDirectory.HttpModules.AuthenticationModule, DotNetNuke.Authentication.ActiveDIrectory" />. Don't worry that it's not in your web.config before you do your initial install or upgrade to 4.6.0 as it's added when the provider is installed. However, do not uncomment the original Authentication line as it will cause problems down the line.
Once the provider is installed and enabled as an available provider (this can be checked under Host->Host Settings->Authentication Settings) the settings can be set under Admin->Authentication as per the pinned post in the Active Directory forum. Unfortunately you will also need to redo the Authentication settings in the case of an upgrade from 4.5.5 or lower.
Lastly, if you were using automatic logins you'll have to set the permissions for Windowssignin.aspx as it's moved from Admin/Security to DesktopModules/AuthenticationServices/ActiveDirectory.
I will get some formalized documentation posted sometime this week but, as always, feel free to ask questions in the Active Directory Provider forum.