Bahmni EMR component runs on top of OpenMRS, and therefore OpenMRS becomes the data model for Bahmni EMR. Therefore many configurations will end up being OpenMRS configurations, and will likely be updated from OpenMRS Admin screen.
But there are also UI modifications to Bahmni, like plugging in some app, or deciding UI defaults etc on screen in Bahmni, which are not related to OpenMRS, but are Bahmni EMR UI only configurations. In those cases the config will unlikely belong to OpenMRS AdminUI, and instead require Bahmni configuration via Bahmni JSON config files.
Please refer to this video, and this documentation to know more about Bahmni Configuration.
The Implementers Guide on wiki is dedicated towards explaining how an implementer can make configuration changes to Bahmni to suit their requirements.