Identifying three wires for two bulb fixture
There should only be a single hot wire for a three way switch.  The other two wires are known as "travelers" connecting the two switches. I would disconnect all of the wires and ohm them out one at a time from switch to fixture and fixture to fixture.  

At the very least, disconnect power, disconnect the wires at the fixtures, and check for power.  Once that is identified, the other two will be a quick swap if you guess wrong and nothing will get damaged.

Either way, once identified, you should be able to mark and reconnect them  correctly.