1. Make sure the Combination Facets module is installed along with the Standard Facets module. 

2. Make facet custom field codes start with facets_ for easy organization. Such as facets_color

3. Check the "facets" box when creating facet custom fields (duh)

4. Load info into the facets custom fields the same way as anything else.

Facets Template

Unfortunately the facets template is now part of sequences. However, the facets template in the User Interface Global Settings can still be used. Remove the sequence facets call and replace with <mvt:item name="facets" /> to use the global facets template. It will probably work by default with all the sorting dropdowns and whatnot on the CTGY and SRCH pages.