Confusion about ccfl inverter transformer
The primary can be any physical location/pin on the transformer and ditto the secondary. The only constraint is that if you expect a decent level of voltage isolation then make sure you use enough "distance" between primary pins along one edge and secondary pins along the same edge. Looking at your picture in detail I'd say this design was good for a 1000 volts: -



Probably the bigger issue would be with the PCB with what is called "tracking" of high voltage PCB traces with low voltage ones.