How can you distinguish the source of Bitcoins?
Whenever a payment is sent to an address, it is received as a distinct transaction output. It should be a trivial task for the FBI to label the output or outputs accordingly to know which were created in the confiscation of Silk-Road's funds.

On the other hand, there is no such thing as the "actual coins". Whenever bitcoins are transferred, the outputs that feed the transaction are destroyed and new transaction outputs are created.