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They would be different colours to signify *how to pair the modules in different channels*.  If you have 4x2GB modules, of course you will be using all the slots so it doesn't matter, but if you had 2x4GB modules you'll want to make sure that you have a module in both channels to take advantage of the dual channel memory benefits. 

EDIT: The channels on this motherboard are channel 0: DDR3_1 and DDR3_3 and channel 1: DDR3_2 and DDR3_4.  So yes if you only have 2 modules put them both in the white banks as they are different channels.