The flow of two immiscible fluids completely filling an enclosed cylinder and driven by the rotation of the bottom end wall is studied numerically. The simulations are in parameter regimes where there is significant advection of angular momentum, i.e., the disk rotation rate is fast compared to the viscous diffusion time. We consider two classes of scenarios. The first consists of cases that are straightforward to reproduce in physical experiments where only the rotation rate and the viscosity ratio of the fluids are varied. Then we isolate different forces acting on the system such as inertia, surface tension, and gravity by studying variations in individual governing parameters. The viscosity ratio determines how quickly the upper fluid equilibriates dynamically to the flow in the lower fluid and plays a major role in determining how vortex lines are bent in the neighborhood of the interface between the two fluids. This in turn determines the structure of the interfacial layer between the two swirling fluids, which is responsible for the flow in the upper fluid. The simulations show that even when there is significant interfacial deformation, both the dynamics and the equilibrium flow are dominated by vortex bending rather than vortex stretching. The simulations show that for the range of immiscible fluids considered, surface tension effects are significant. Increased surface tension reduces the degree to which the interface is deformed and the limit of zero surface tension is not an appropriate approximation.