It doesn't really matter which source goes to which ear, it's matter of personal preference... as long as the two sources are SEPARATE on two different ears, not on top of each other.
On the old mixer I have, two sources are separate during cueing. As you push up the volume on the new track, the sounds are merged together on the headphone, just like the master.
On all the controllers I've played with, the two sources are ALWAYS mashed together during and after the cueing.
Now if I have Virtual DJ send its 'headphone outputs' to my computer speaker, then it's perfect!
I *could* plug my headphone into the computer speaker's headphone out but that would kill the sound from the speaker and therefore requires that I plug my headphone in and out for EACH song. That would be crazy!