  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, 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) optical lattice clock 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 $2.4(1) \times10^{-17}$ between two ensembles, useful for
characterization of intra-lattice differential systematics.
