You may want to start with the configuring logstash docs to get an idea as to how this process looks. It involves creating a .conf file, which you can do from the command line.
Also for your case, perhaps this thread, though old, would be even more useful: How to process "Lat" & "Long" fields using default Logstash config and mapping to use in Kibana 4 tile map
It includes a link to this blog post which gives some concrete examples of using mutate to turn separate latitude and longitude values into a geo_point location.
(I'm going to re-categorize this discussion under Logstash since it's more relevant to ingesting data... hope that's okay!) 