A critical aspect and differentiator of a System of Systems (SoS) versus a single monolithic system is interoperability among the constituent disparate systems. A major application of Modeling and Simulation (M&S) to SoS Engineering is to facilitate system integration in a manner that helps to cope with such interoperability problems. A case in point is the integration infrastructure offered by the DoD Global Information Grid (GIG) and its Service Oriented Architecture (SOA). In this chapter, we discuss a process called DEVS Unified Process (DUNIP) that uses the Discrete Event System Specification (DEVS) formalism as a basis for integrated system engineering and testing called the Bifurcated Model-Continuity life-cycle development methodology. DUNIP uses an XML-based DEVS Modeling Language (DEVSML) framework that provides the capability to compose models that may be expressed in a variety of DEVS implementation languages. The models are deployable for remote and distributed real-time executing agents over the Service Oriented Architecture (SOA) middleware. In this paper, we formulate a methodology for testing any proposed SOA-based integration infrastructure, such as DISA's Net-Centric Enterprise Services. To support such a methodology we use DUNIP to define a Test Instrumentation System (TIS) that employs the DEVS/SOA infrastructure to deploy agents to test the mission success and performance levels of collaborations over the GIG/SOA.