Some modules have their own configuration. e.g you can create project categories, time and expense codes, enter billing rates, user cost rates and so on.
Project Management (Read Project Categories (Section 7.1), Custom Fields (Section 7.1.3))
Timesheet (Read Time Codes (Section 10.6), User Cost Rates (Section 10.4), Billing Rates (Section 10.5))
Expenses (Read Expense Codes (Section 11.1.1))
Workflow (Read Workflow Admin Guide from the main help section)