Thank you so much ergotherego. For the people that find this thread with the same question here is what you do:
Once you have the FortiGate in the list of devices you need to make sure you "Import Policy" under Device Manager and highlight the unit you want to import the settings from. This is so that you get all the ports listed under: Policy & Objects>Object Configurations>Zone/Interface>Interfaces
What ergotherego is referring to is that once you have those interfaces in there then create some zones. This is the most important part because you will add ports to the Zone and then you reference the Zone name in the policies and then you assign the policy to a device and that is how the mapping occurs.
So you create a zone in the same Interfaces menu you are by clicking Create New>Zone at the top menus. Name the Zone whatever you want, for example: OfficeLAN, OfficeDMZ, DataCenterWAN, DataCenterLAN, etc...
Then, in the same location, double click the Zone, Switch On the Per Device Mapping, Add, select the device and the port. You get a message that it will change the current mapping, select yes, and voila!
Run the Install Wizard and you will see the ports and zones you created reflected on the device. Create you policies using the Zone Names.
Another way to look at it is like this is with this example:
FortiGate1 has 2 ports
Fortigate 2 has 4 Ports
FortiGate 1 (Office) > P1, P2
FortiGate 2 (DataCenter) > P1, P2, P3, P4
Create a zone that will be used in the office for WAN and LAN and another in the DataCenter for the same WAN and LAN
Create the Zone and assign the ports
OfficeWAN > P1
OfficeLAN > P2
DataCenterWAN > P1
DataCenterLAN > P2
You will effectively see P1 and P2 mapped both of the devices but you will call your Zones independently in the Policy Package that will be assigned to a Device.