In this thesis, I present experiments on making and probing strongly correlated gases of ultracold atoms in an optical lattice with engineered potentials and dynamics. The quantum gas microscope first developed in our lab enables single-site resolution imaging and manipulation of atoms in a two-dimensional lattice, offering an ideal platform for quantum simulation of condensed matter systems. Here we demonstrate our abilities to generate optical potential with high precision and high resolution, and engineer coherent dynamics using photon assisted tunneling. We also create a system of bilayer quantum gases that brings new imaging capabilities and extends the possible range of our quantum simulation.