Wavefront shaping can tailor multipath interference to control multiple scattering of waves in complex optical systems. However, full-wave simulations that capture multiple scattering are computationally demanding given the large system size and the large number of input channels. Recently, an ``augmented partial factorization'' (APF) method was proposed to significantly speed-up such full-wave simulations. In this tutorial, we illustrate how to perform wavefront shaping simulations with the APF method using the open-source frequency-domain electromagnetic scattering solver MESTI. We present the foundational concepts and then walk through four examples: computing the scattering matrix of a slab with random permittivities, open high-transmission channels through disorder, focusing inside disorder with phase conjugation, and reflection matrix computation in a spatial focused-beam basis. The goal is to lower the barrier for researchers to use simulations to explore the rich phenomena enabled by wavefront shaping.