Enterprise IT environments are complex: business applications rely on distributed middleware running on diverse hardware with components depending on each other in many unexpected ways. Discovery of applications' dependency on IT is a critical step in managing application and IT infrastructure together. Many tools and practices have emerged to discover and report IT assets and applications' dependency on the IT assets. However, our experience in the field shows that there are significant challenges in effectively deploying the tools. There is a critical need to research and develop flexible processes, methods, and practices, and architecture-level support for them in the tools to enable successful discovery using a "built-to-order" approach. In this paper we discuss our experiences with an advanced application-data relationship discovery tools in large scale enterprise environments and based on these experiences we identify three main challenges of effective discovery. They are: deployment process and related security issues; unavailability of software and administration-related information; and tool integration. To address these challenges, here we demonstrate a holistic approach that includes flexible processes, methods, and practices in the tools for achieving the necessary built-to order capability.