You should start your Active Directory design with the namespace. However, you will not be able to complete the logical namespace design until you have the physical design sketched out. It's very much a chicken-and-egg situation. You should plan to go through and complete a rough draft of the namespace design, then make a rough draft of the physical design, then consider modifications to both.
Next you can consider the Group Policy Object (GPO) design. Group Policy Objects control such things as user-environment lockdown, forced registry changes, application availability, and so on, to sets of machines or users. Because these relate to sites, domains, Organizational Units, users, computers, and groups in your Active Directory, it makes sense in my experience to incorporate these changes into a namespace and site design that already exist.
You can then take a look at security and at tailoring Active Directory to your own requirements by modifications to the Schema. Finally, this section takes a brief look at the present and the future of integrating and interoperating Active Directory with other directories and operating systems and of migrating to Active Directory.