I find that even with custom dice it helps to have two sets of colors. Maybe a full set of one color and a half set of another to help speed up with rolling.
With my Eldar I have red and black dice- when I roll for my vypers I use black dice for the shuriken cannons and red dice for the star cannons- helps to speed up the rolling.
One set of colors for regular attacks, the other for power weapons? Once for storm bolters, and the other for assault cannons- makes different weapons in the same unit a bit quicker to handle.