Systems with short-range attraction and long-range repulsion can form ordered microphases in bulk and under confinement. In fact, confinement has been proven to be a good strategy to induce the formation of novel ordered microphases that might be appealing to the development of functional nanomaterials. Using Grand Canonical Monte Carlo (GCMC) simulations, we study a model colloidal system with competing interactions under confinement in narrow spherical shells at thermodynamic conditions under which the hexagonal phase is stable in bulk. We observe the formation of three parent ordered structures formed by toroidal clusters and two spherical clusters (Type I), toroidal clusters and one spherical cluster (Type II), and toroidal clusters alone (Type III), depending on the radius of the confining shell, that can often coexist with other related structures derived from these parent ones by a simple transformation, in which the system is divided into two hemispheres that are rotated with respect to each other by a given angle. We propose a general method to characterize and predict the structures obtained under confinement in spherical shells in systems able to self-assemble into a hexagonal phase in bulk. We also show that deforming the spherical shells into ellipsoidal ones affects the structure of the system in such a way that helical structures are favoured by prolate ellipsoids and toroidal structures by oblate ellipsoids.