According to the specification, the 480 V winding will be around 500 Ohms. The mains winding will be around 15 Ohms. You should be able to identify those on the basis of their resistance. The low voltage windings are really low resistance so could be easily confused.
If you avoid the low-resistance windings, and you have a 1 or 2 A slow-blow fuse in circuit, it will be hard to damage the transformer. If you power the 480 V winding with 120 V mains, you will just get around 30 V from the mains winding, and 1 - 1.5 V from the others.
Once the transformer is powered, you should be able to find which is the 6.3 V winding and which is the 5 V winding from the voltages they produce. With no load I would expect them to be 10 - 20% higher, so you might get around 7 V from the 6.3 V winding and around 6 V from the 5 V winding.