In every PSU I've looked at inside, all the black wires went to the same copper area on the circuit board. All wires of the same color are like this, except if they're the voltage sensing wires that are paired up with another wire (usually thicker) in the same connector pin (almost always one of the wires paired up with an orange wire, and it may be orange or brown, but I've seen a sense wire paired with a +5V red wire and even with a black ground wire), but I speculate that some high power supplies split some wires of a given color into two groups, each with its own current limiter (I've read that yellow +12V wires can be like this).
It should not be a problem. Statistically, I am pretty sure I have done it because I have undone molex connectors to put sleeves and never paid attention to the blacks initial location. It does not matter. Both, 5V and 12V have to share the same ground, so the grounds have to be connected in the PS.