Are people that are working on the security aspects of your design finding that it is better to structure those aspects of the design into other aspects of the design, or create a separate section that gives diagrams and requirements for security separately from other parts of the design?
In other words:
-Logical Network design with security aspects built in
-Physical Network design with security aspects built in
-Logical Network design
-Physical Network design
-Seperate security design section detailing firewall, A/V, and other security related aspects with diagrams showing how specific security requirements are satisfied by this design.