Depending on the type of your organization, the way that you setup your initiatives will be different.
Here are 3 different initiative structures based on the type of organization:
Agencies (Consultants, Marketing, Design, Website, Software)
An initiative can be a Client's name. You can then create multiple projects below which either run in parallel, or one after another.
Enterprise & IT Departments
An initiative can be a Business Unit or a Department. Each department runs their own projects. Resources can be shared across initiatives.
Companies Developing Products
An initiative can be a Product. You can run multiple projects inside each initiative.