With Partition Commander 10 Pro/Server and later versions, yes, you will be able to repartition USB/Firewire external drives.
As long as your OS sees these drives correctly.

Partition Commander 8/9 is not able to partition USB/Firewire external drives.
These drives are not recognized by the computer's BIOS upon initial bootup.
Drivers for USB/Firewire drives are loaded when Windows boots.
Partition Commander 8/9 can only see what the computer initially sees upon bootup.