As the two-body heaving wave energy converter (TBH-WEC) moves toward more commercial and large-scale applications, it usually has to be deployed in the form of arrays to reduce costs and achieve better performance. However, hydrodynamic interactions in TBH-WEC arrays are highly complex and difficult to evaluate. The effect of array configuration on the performance and interactions of TBH-WECs within the array has not been fully investigated. To address this gap, the power output time-domain modeling of TBH-WEC arrays is first established using the enhanced MATLAB-APDL-AQWA unified simulation system. Based on this system, this work investigates the internal relationship between incident wave frequency, array size, array layout, and Power Take-Off (PTO) system, and array interaction factors in both unidirectional regular and irregular waves, as well as multidirectional real-wave scenarios. The energy redistribution properties of the array wavefield are then analyzed, as is the correlation between array layout and the disturbance wavefield of the devices. Results show that array layout optimisation and PTO configuration optimisation are relatively independent from each other, and that better array layouts can be quickly obtained by iteratively adding clusters or devices in the amplified region of the existing array disturbance wavefield.