Just for simplicity , lets say we have a 230 volt primary and a 230 volt secondary , it wont make any difference which way round you connect input or output cables , in the case of dual windings for p[arralel or series connection , in series the end of one coil connects to the start of the other , in the case of parralel you need both windings in phase,in other words both start wires and both finish wires commoned , if you get the windings the wrong way ,one wire feeds phase + the other feeds phase - ,the result is cancelation ,and I think the transformer wont be long overheating and dying . You always need to pay attention to the start and end of coils for series or parralel opperation of either primary or secondary windings .
In the case of an output transformer you also need to pay close attention to way its wired , for instance lets say you swap the ground wire on the secondary of an output transformer ,if you happen to have negative feedback across the transformer ,back to an earlier stage ,your amp will almost certainly oscillate badly , this is because if you reverse the wires it means your negative feedback becomes positive , and instead of the gain being reduced the gain is increased to the point where your amplifier becomes an oscillator.
A common phasing issue is where someone inexperienced wires hifi speakers wrongly , if you have your speakers out of phase all the bass drops away ,one speaker is pushing the air the other is pulling it so at various points in the room bass will almost dissappear ,people vary in their abillity to even detect it sometimes ,its not so noticeable at high frequencies, but the stereo image kinda collapses in on itself and sounds hollow ,I know its not the original question you asked ,but it serves as a metaphor to the other examples above .
If you got no hum ,leave it just as it is , using the three secondaries the way you are seperately means it wont be an issue ,normally on the primary the label says which coloured wires to link for 110 or 220 so theres no chance of doing it wrong ,or maybe less chance at least ;D
