If you are using a custom output plugin, it must be set to the AgRt3Application Output property; if you are using RT3 inside of a STK Engine-based application however, no further initialization is necessary. Note that AgRt3Application and AgRtGlobals are both singletons.
AgRtGlobals m_RtGlobals = new AgRtGlobals();
AgRt3Application m_Rt3 = new AgRt3Application();
m_Rt3.Output = MyOutputPlugin;
STK 11.2.1 Programming Interface