Its dependent on the circuit . Some times a secondary winding falls back to the High side of the SMPS to power the PWM.With these high frequency transformers its much harder to know by the resistance alone because of fewer winding s .Some can have as few as a half winding on a secondary.If its still in circuit the primary will be on the high side (mains input side) and will be tied to the drains of one or more MOSFETS and will have larger copper traces.If theirs a secondary on the high side will most likely be,but not directly , linked to the PWM .All remaining secondaries will be on the low voltage side.Think of the transformer as the border between the high voltage side and low voltage side.
If the transformer is out of circuit and your unsure of the orientation then a arbitrary function generator can be used to find the pin outs of the transformer.If you have a function generator.