Cable Side and Physical Side of a PoE Magnetics
In its datasheets, e.g. this, Pulse Electronics typically labels the chip side circuits with D letter while it labels the medium side circuits with X letter: TD+ &lt;-&gt; TX+, TD- &lt;-&gt; RX-, ect...

Therefore, pins 1,2,3,6,7,8 of an H(X)2260NL transformer are (nominally) chip side pins. If you need an oppositely crossed one, have a look on H(X)1260NL.


  It looks like Common mode choke should be facing the cable side (away from Ethernet controller). Is it correct statement?


It is application dependent. No single method exists. In your case, Pulse's PoE-enabled transformers H(X)2260NL and H(X)2305NL implement CMCs at the chip side.