Recently, cyclorotors, utilizing lift rather than buoyancy forces for energy extraction, have been proposed and inherit many of the appealing features characteristic of modern wind turbines. In particular, the ability to spill energy though foil pitching allows the device to remain at rated power despite significant variations in input power level, while additional cyclorotor features, including variable submergence depth and rotor radius, also permit a significant degree of modulation of the device structure, and energy absorption characteristics, offering considerable flexibility. These configuration flexibilities, in addition to torque control of the rotor/generator shaft (also characteristic of wind turbines) offers the control engineer considerable freedom in adjusting the device characteristics to maximise the effectiveness of the device in capturing wave power, while maintaining structural integrity and minimizing harmful stresses on system components. However, such flexibility also provides a significant challenge in the form of a multivariable control problem for a system described by significantly nonlinear hydrodynamics. This paper describes a proposed hierarchical control system for a cyclorotor wave energy device, utilizing submergence depth, rotor radius, foil pitch angles, and shaft torque as control inputs. The hierarchy involves the separation of the control actuators into two classes: structural (or slow) control effectors, and wave-by-wave (or fast) control effectors. In particular, the paper will examine the interaction between the two levels of the control hierarchy and the need, if any, for simultaneous optimisation of the control parameters at both levels.