As far as I know, multiple layers with Leaflet isn't possible at the moment.
However, if you're wanting to differentiate between items of the same type but with different taxonomy tags, the module "IP Geolocation Views and Maps" (https://www.drupal.org/project/ip_geoloc) will allow you to do this. They've got excellent instructions and I can vouch for it working.
It can get confused if an item is tagged with 2 of the things you're wanting to differentiate between...