The design of complex systems involves many engineering disciplines, and many different tools and formalisms. Solutions such as IBM Rational Engineering Lifecycle Management(RELM) present a unified view of information collected from multiple tools. Various queries and reports are predefined, but engineers need to define their own custom queries, based on their specific processes or products. This paper presents a classification of various types of useful queries and rules over the combined information. Some rules could not be expressed precisely, because of missing information in the repositories. Other rules had to be stated at a lower level of abstraction than desired, because of the level of the concepts in the repository. The paper gives examples and suggests ways to remediate these issues. A visual query formalism based on SysML object diagrams to express these queries is described. The visual query language has been implemented and used to express rules and find violations in two repositories.