How to properly use a Balun?
One instance wires the thing as a balun (Common mode choke), the second case is a transformer...

Usually you see the transformer configuration used up to maybe a 150MHz or so, with the balun configuration employed once things get fast, but your best approach is probably to try it both ways and see what the network analyser has to say. 

The transformer configuration can be useful when DC isolation is desired, the balun when the non ideal nature of VHF transformers becomes a problem.