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Engineering symmetry in 2D materials has recently emerged as a promising way to achieve novel properties and functions. Here we report the in-situ integration of AA’ and AB stacked bilayer MoS₂ with different inversion-symmetries by creating atomically sharp stacking boundaries between the differently stacked domains, via thermal stimulation and electron irradiation, inside an atomic-resolution scanning transmission electron microscope. The setup enables us to track the formation and atomic motion of the stacking boundaries in real time and with ultra-high resolution which enables in-depth analysis on the atomic structure at the boundaries. In conjunction with density functional theory calculations, we establish the dynamics of the boundary nucleation and expansion, and further identify metallic boundary states. Our approach provides a means to synthesize domain boundaries with intriguing transport properties, and opens up a new avenue for controlling valleytronics in nanoscale domains via real-time patterning of domains with different symmetry properties.