The CuCr1-xInxP2S6 system represents a large family of metal chalcogenophosphates that are unique and promising candidates for 2D materials with functionalities such as ferroelectricity. In this work, we carried out detailed microstructural and chemical characterization of these compounds using aberration-corrected STEM, in order to understand the origin of these different ordering phenomena. Quantitative STEM-HAADF imaging and analysis identified the stacking order of an 8-layer thin flake, which leads to the identification of anti-site In(3+)(Cu(+)) doping. We believe that these findings will pave the way towards understanding the ferroic coupling phenomena in van der Waals lamellar compounds, as well as their potential applications in 2-D electronics.