The LANSCE Refurbishment Project (LANSCE-R) is a phased, multiyear project. The project is scheduled to start refurbishment in the 2nd quarter of fiscal year 2011. Closeout will occur during the 4th quarter of FY2016. During the LANSCE-R project, installation of project components must be scheduled during six annual 6-month maintenance-outages and not conflict with annual LANSCE operational commitments to its user facilities. The nature of a major refurbishment at a facility with production commitments requires carefully planning the system installation, functional testing and commissioning responsibilities, and the transition to operation. This paper will report on the systems engineering approach to the integration and control of 1) Engineering Activities, 2) Performance and Design requirements, 3) Interface Control, 4) Technical Assurance, 5) System Integration, 6) Configuration Management, and 7) Operational Planning, Startup Testing, and Installation. A particular focus will be given to the Controls, Instrumentation and Diagnostic Systems.