If you have some feedback please post to my Google+ post referencing this issue:
The attachment you can download is a copy of the code I used for the map.
For my example I am using Public data from DC GIS Catalog, specifically the Washington DC Metro lines and Stations.
Initially I used FusionTables Layer Builder which helped me figure out how to layer two layers in the same map. I quickly learned how to layer multiple layers by mirroring the code referencing the tables.
Next step I have to cleanup the code and learn a little styling for background color behind the check boxes.
FusionTables Info if it helps:
DC Metro Stations Table ID: 2193846
DC Metro Lines Table ID: 2193391