Chapter 10 Install and System Administration for FortiOS 5.0 : VLANs : VLANs in transparent mode : Configure the FortiGate unit
  
Configure the FortiGate unit
The FortiGate unit must be configured with the VLAN subinterfaces and the proper security policies to enable traffic to flow through the FortiGate unit.
See Also
Add VLAN subinterfaces
Add the security policies
General configuration steps