Hi Joe -
Unfortunately, you'll need to poke about in the file structure of Funnelback to apply any changes to a meta collection's faceted navigation configuration.
After you're happy with the structure of your meta collection's faceted navigation (you can still edit the config via the Admin UI), you'll need to copy that config into the stem of the live index via the command line, renaming as you go:
cp $SEARCH_HOME/conf/META-COLLECTION-ID/faceted_navigation.cfg $SEARCH_HOME/data/META-COLLECTION-ID/live/idx/faceted_navigation.xml
Ordinarily, this step is automatically performed whenever a collection updates - as meta collections never update, there's no straightforward means of applying this step via the Admin UI or as an automatic task.
Other workarounds may include running that command above as a post-update workflow task for one of the component collections, or creating a symbolic link to the faceted navigation config from another non-meta collection.
You can manage the gscopes.cfg in a central meta collection, but you'll need to inform each component collection of the location of that gscopes file. This could be desirable if several collections are inheriting the same set of gscopes.
# $SEARCH_HOME/conf/COMPONENT-COLLECTION-ID/collection.cfg
post_index_command=$SEARCH_HOME/bin/padre-gs $SEARCH_HOME/data/COMPONENT-COLLECTION-ID/offline/idx/index $SEARCH_HOME/conf/META-COLLECTION-ID/gscopes.cfg
See also:
https://docs.funnelback.com/11.4/post_update_command_collection_cfg.html
https://docs.funnelback.com/11.4/gscopes.html