In this article we investigate the morphology and manipulation of monodisperse emulsions at high dispersed phase volume fractions (gel emulsions) in a microfluidic environment. Confined monodisperse gel emulsions self-organize into well-ordered droplet arrangements, which may be stable or metastable, depending on the geometry of the confining microchannel. Three arrangements are considered, in which the droplets are aligned in a single file, a two row, or a three row arrangement. We explore the potential for induced transitions between these distinct droplet arrangements as a tool for droplet-based microfluidic processing. Transitions are readily achieved by means of localized (geometrical) features in channel geometry, however the onset of the transition is strongly dependent on the subtleties of the microfluidic system, e.g. volume fraction, droplet size, and feature dimensions. The transitions can be achieved via fixed channel features or, when the continuous phase is a ferrofluid, by a virtual channel constriction created using a magnetic field.