Previously I commented that Fusion 6.0 does not support adding additional hard disks to a linked clone. This is a pretty bad limitation, and it does not make sense. This is supported with VMware Workstation 10.
When you attempt to add a disk you see the following:
I have found a way to force Fusion 6.0 to support this.
Step 1:
You must first create a VMDK file using a different VM that is not a linked clone.
Step 2:
Once you have created the additional disk, you then must show the package contents of your VM, grab the newly created VMDK file and move it to the container of the linked clone VM
Step 3:
Now you must edit the linked clone .VMX file to manually add the additional configuration lines to the file.
For my situation, I am using SATA for the bus, and I wanted to use a different SATA bus number than the one that the linked clone is booting from.
sata1.present = "TRUE"
sata1:0.present = "TRUE"
sata1:0.fileName = "Virtual Disk 2.vmdk"
sata1:1.present = "TRUE"
sata1:1.fileName = "Virtual Disk 3.vmdk"
You may need to change your Bus or Device IDs from what I am using here.
Save the file. When you view Fusion settings for the VM you should now see the additional disks...
Now you can boot up the VM and use Windows Storage Manager to create volumes and format them.
This feature should be supported out of the box without requiring manual edit of the VMX files!
VMware Workstation 10 provides this feature. Fusion 6 should as well.