When configuring the facets, all changes should be made in the "Facets" configuration section of the Algolia Shopify app, under Search Options > InstantSearch > Customize > Facets. This will show all of the default facets, along with any custom facets that have been added via Named Tags or Metafields.
To make the filterOnly facets not display in frontend, you can make the facet hidden in our plugin under Search Options > InstantSearch > Customize > Facets. Click edit on the facet that you would like to change to filterOnly and change it to 'hidden'. This way, the facet will still get added to the attributesForFaceting setting, but not displayed on the search page.