Thanks! The recommended way to get additional fields indexed at the moment is to add them to "tags": Agent API | APM Node.js Agent Reference [4.x] | Elastic
For some fields that might be impossible or very inconvenient. It turns out that unfortunately 6.4 introduced a small bug which requires that you set setup.template.fields to fields.yml in order for apm-server to load the file. I've filed an issue fields.yml is ignored but still shipped with packages · Issue #8607 · elastic/beats · GitHub.
Please also make sure you've set setup.template.overwrite: true and that it only works for newly created indices.
Let me know if that helps.
/Ron