LotAtc Advanced supports themes now. You can switch theme at any time (no need to restart the app).
Use top right button that display current server profile.
Only with LotAtc >= 2.2.0, documentation is in progress
You can also change mission directly from LotAtc Advanced:
You can interact with DCS mission flags that are exported in LotAtc. See this page to see how to register a flag in mission script.