Hi Matthew,
As you noticed, so-import-pcap configures Logstash to use the /etc/logstash/conf.d.ingest.output/ directory. This is a minimal Logstash config where Logstash doesn't really do any parsing, it simply sends logs to Elasticsearch and that's where the parsing occurs. This is what allows so-import-pcap to run in a much smaller amount of RAM with a quicker Logstash initialization time than traditional Logstash parsing config. So you have a couple of options:
1. remove the LOGSTASH_OUTPUT_INGEST option from /etc/nsm/securityonion.conf. You should be able to configure Logstash as you would with live network monitoring, but keep in mind that it will require more RAM and Logstash initialization will be slower.
2. the better option would probably be to perform your tagging via Elasticsearch ingest node. See our existing parsers in /etc/elasticsearch/ingest/ for examples.