The most important ATLAS upgrade for LHC run-3 has been in the Muon Spectrometer, where the replacement of the two forward inner stations with the New Small Wheels (NSW) introduced two novel detector technologies: the small strip Thin Gap Chambers (sTGC) and the resistive strips Micromegas (MM). The integration of the two NSW in the ATLAS endcaps marks the culmination of an extensive construction, testing, and installation program. The NSW actively contributes to the muon spectrometer trigger and tracking. Hence the concurrent finalization of the commissioning phase of this innovative system and the optimization of its deployment will be presented here. This proceeding will offer an overview of the strategies employed for reconstruction, integration and optimization, followed by a detailed report on the performance studies of the NSW system during its initial operation with LHC Run3 data.