You don't. Settings.bundle is supposed to be created at compile time, and is fixed (as well as signed as part of the application build process.)
See the Settings.bundle documentation which explicitly states (emphasis added):
A Settings bundle has the name Settings.bundle and resides in the top-level directory of your app’s bundle.
The emphasized part is what tells me you can't put the bundle anywhere else. This answer confirms what I just said.
Conditionally displayed settings are also not possible.