Dam these are so confusing…
https://support.plex.tv/articles/200241558-agents/
The agents that plex uses for scanning meta data, you will find them in Settings > Agents
The problem is that half the time you get told to disable the local media agent to prevent the embedded data in the mp4 files from being read by plex, as it will use this rather than the info it got from the online media source.
You need to local media agent to be enabled if you want plex to pick up external subtitles. Just spent an hour trying to work out why subtitles were not showing on 2 of my servers while 1 was fine. Turned out that agent was unchecked.