The tight packing does not really allow to solder in two molex connectors anyway, so just have one per motor output and have them all in one line not offset.
Also: number them through motor 1, motor 2, ... which makes it easier for the axis-mapping explanation.
Don't name the pololus X, Y, Z etc, as this is not accurate anymore, just call it channel 1, channel 2 or ch-1, ch-2 or something.
The tight packing does not really allow to solder in two molex connectors anyway, so just have one per motor output and have them all in one line not offset.
Also: number them through motor 1, motor 2, ... which makes it easier for the axis-mapping explanation.
Don't name the pololus X, Y, Z etc, as this is not accurate anymore, just call it channel 1, channel 2 or ch-1, ch-2 or something.