Specification and Requirements
Assessing the needs of an organization is the crucial first step. Take the time to do a thorough survey of what is currently in use within your organization. Think long and hard about how closely this matches your true needs. Make sure that everything is well-defined in terms of behavior and that all tasks and use cases are described clearly. Capture the work-flow. Play around with the user interface, including mock-screenshots.
Architecture and Design
After you know what is needed, the next step is describing how those goals will be attained. Develop a database schema. Diagram the data flows. List out all the components of the system. Detail the interfaces between components. Copious diagrams will be used.