Recently, covariance analysis has found significant use in the field of chemical reaction dynamics. When coupled with data from product time-of-flight mass spectrometry and/or multi-mass velocity-map imaging, it allows us to uncover correlations between two or more ions formed from the same parent molecule. While the approach has parallels with coincidence measurements, covariance analysis allows experiments to be performed at much higher count rates than traditional coincidence methods. We report results from electron-molecule crossed-beam experiments, in which covariance analysis is used to elucidate the dissociation dynamics of multiply-charged ions formed by electron ionisation over the energy range from 50 to 300 eV. The approach is able to isolate signal contributions from multiply charged ions even against a very large 'background' of signal arising from dissociation of singly-charged parent ions. Covariance between the product time-of-flight spectra identifies pairs of fragments arising from the same parent ions, while covariances between the velocity-map images ('recoil-frame covariances') reveal the relative velocity distributions of the ion pairs. We show that recoil-frame covariance analysis can be used to distinguish between multiple plausible dissociation mechanisms, including multi-step processes, and that the approach becomes particularly powerful when investigating the fragmentation dynamics of larger molecules with a higher number of possible fragmentation pathways.