Design Structure Matrices (DSMs) are a widely spread and useful tool for structuring and analysing design processes and related aspects such as products themselves, organisations, etc. Though this tool is simple, yet quite powerful, problems might arise in using them due to the subjectivity of the set up model within the DSM, as it is with every model building exercise. This contribution looks at the individual differences in filling out a DSM, the reasons for those differences, as well as means to overcome them. This covers a clear procedure for using DSMs, extended tools using and supporting DSMs, and a better understanding of this matrix approach. The latter covers different issues and “linkage types” that can be addressed by a DSM and its use in a system theory context. It also emphasises that DSMs are just one method using a matrix approach, which is only one representation of a graph or a network, with other methods using similar approaches and covering other useful aspects. A simple, yet important contribution of our research is the appropriate direction of DSMs, i.e. the dependencies going from rows to columns or vice versa, since this is an often discussed subject concerning DSMs.