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Flight Tracking is the plugin that tracks your pilots’ flights and files their PIREPs, so every pilot has it and it can’t be removed. Its Settings tab changes how tracking behaves for everyone at your airline. Most airlines only need to look at Time capture; the rest have sensible defaults. Open it from Plugins → Flight Tracking. Its other tabs are Event rules and Additional fields.
Flight Tracking's settings for the airlineFlight Tracking's settings for the airline

The settings

Settings save as you change them. They’re grouped under Position updates, Flight time and fuel, Pilot permissions and Online networks.

Allow Start anyway and your flight-start API

Allow Start anyway also governs your airline’s own confirmation dialog. When your flight-start API returns a confirmation message, its “Start tracking anyway” button follows this setting. Your API can return can_override on /flights/start to decide for one start: true always allows the bypass, false always blocks it, and leaving it out falls back to this setting.

Online networks

While Ask which network pilots are flying on is on, the list below it sets the networks pilots choose from. Shown to pilots is the name they see and Sent as is the value your backend gets. Offline is always first and always sent as offline; only its name can change. Add network adds one, the handles reorder them, and Reset to defaults puts back the standard list (VATSIM, IVAO, PilotEdge, POSCON, BeyondATC and SayIntentions AI).

What pilots set themselves

Pilots choose some settings for themselves in Stratos, such as Auto-Start Tracking and Auto-Submit Flight. They’re listed under Set by each pilot at the bottom of the tab, for reference.