A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-substrate junction. A cell-substrate junction is a specialized region of connection between a cell and the extracellular matrix. [ http://www.ncbi.nlm.nih.gov/pubmed/10419689 http://www.ncbi.nlm.nih.gov/pubmed/26923917 http://www.ncbi.nlm.nih.gov/pubmed/16805308 http://www.ncbi.nlm.nih.gov/pubmed/1643657 http://www.ncbi.nlm.nih.gov/pubmed/8314002 ]