As far as i know it does make a difference, the one in the neck needs to have the wires towards you (when the guitar is laying infront of you) while the bridge one should have the wires towards the pots (away from you). They sound brighter in one direction (don't remember which).
From DiMArzios Website
Does it matter which direction I install my pickup?
Most humbuckers are symmetrical and their sound does not change at all when installed backwards, but some have a slightly different sound if you install them in the opposite direction from normal. It’s not a matter of right or wrong, but a matter of taste for such a subtle difference, if you can hear the difference at all. Those models include the Air Norton™, Air Zone™, Evolution® neck, bridge and 7-string, FRED®, Humbucker from Hell™, DLX Plus™ neck and bridge models, Virtual P-90™, Blaze™ neck and bridge models and Tone Zone 7™.
The Steve’s Special™, the Bluesbucker® and the MegaDrive™ have distinctly different sounds if you turn them around, and there is no ‘right’ installation direction. The Bluesbucker® is brighter-sounding with the adjustable screw coil towards the bridge, while the MegaDrive™ is brighter-sounding with the adjustable screw coil towards the neck. The Steve’s Special™ is brighter-sounding if the coil on the pickup’s cable exit side is toward the bridge.