I will describe in situ low-energy electron microscopy (LEEM) studies of graphene synthesis on SiC and polycrystalline Ni substrates. Using spatially-resolved electron diffraction (LEED-IV), we have determined the atomic structure, layer thickness, and stacking sequence of individual graphene domains with sub-micron precision. Using spatially-resolved electron energy loss spectroscopy (EELS), we have correlated the local electronic and atomic structure. I will discuss how these measurements aid in interpreting transport measurements from these same samples. This work was performed in collaboration with Ruud Tromp.