Software intense, complex systems of systems have been the subject of system engineering since the SAGE air defense project and the Atlas guided missile project. The system engineering principles to deal with this engineering challenge have improved greatly over the intervening years. The most advanced set of engineering practices for dealing with software intense complex system of systems has been developed and proven by the software system engineering community. Known as Service Oriented Architecture (SOA) it is a system engineering practice that is not well understood or properly utilized by the general system engineering community. This paper attempts to correct this by both establishing a common understanding of SOA based systems and explaining how the general system engineering community can perform system analysis and system engineering artifact preparation for SOA based systems. The paper is organized into three main topics: the genesis of and definition of SOA based system analysis, the prepare key system engineering artifacts for an SOA based system (for example: CONOPS, SRS, SEMP), and a set of practical principles (heuristics) for applying system engineering to an SOA based system.