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Abstract We demonstrate programmable control over the spatial distribution of ultra-cold atoms confined in an optical lattice. The control is facilitated through a combination of spatial manipulation of the magneto-optical trap and atomic population shelving to a metastable state. We first employ the technique to load an extended (5 mm) atomic sample with uniform density in an optical lattice clock (OLC), reducing atomic interactions and realizing remarkable frequency homogeneity across the atomic cloud. We also prepare multiple spatially separated atomic ensembles, and realize multi-ensemble clock operation within the standard one-dimensional (1D) OLC architecture. Leveraging this technique, we prepare two oppositely spin-polarized ensembles that are independently addressable, offering a platform for implementing spectroscopic protocols for enhanced tracking of local oscillator phase. Finally, we demonstrate a relative fractional frequency instability at one second of $2.4\left(1\right)\times {10}^{-17}$between two ensembles, useful for characterization of intra-lattice differential systematics.