This paper presents a multi-physical system-level simulation workflow to characterise the performance of a heterogeneously integrated communications module for mm-wave applications. Basic principles behind modelling different parts and properties of the module are explained. The workflow combines the electromagnetic properties of a patch antenna array operating at 39GHz with polynomial-based power amplifier (PA) models and thermal simulations of the structural heating. Effects of heating on the PA properties are also considered. The PA model is based on and compared with circuit simulations of a mm-wave transceiver chip, and the results are in good agreement. The proposed workflow can be used to describe and predict the performance of the module in different spatio-temporal use cases, and the approach also scales to larger arrays and more detailed simulation models.