Most settings will be in the registry, so you'd need to figure out where they are in the registry and simply modify them from your program and reload explorer.exe.
Most settings will be in the registry, so you'd need to figure out where they are in the registry and simply modify them from your program and reload explorer.exe.
Other tweaks probably involve patching dll's and then adding your own resources to the existing dll's that load specific resources for the system UI, but of course this probably also invalidates digital signatures in the process and may cause your AV or the Windows AV to raise some red flags depending on what you're doing.