A method and neurostimulation control system for operating two leads disposed adjacent tissue of a patient are provided. A plurality of cross-lead electrical parameters are measured to generate a measured electrical profile of the electrode leads. A plurality of cross-lead electrical parameters are estimated to generate a first reference electrical profile for the electrode leads in a first known staggered configuration. The first reference electrical profile is spatially shifted to generate a second reference electrical profile for the electrode leads in a second known staggered configuration. The measured electrical profile is compared to the first and second reference electrical profiles, and a longitudinal stagger between the electrode leads is quantified based on the comparison.