I am changing my front brakes, and I know how to do it, i've done it a million times on my old civic. However, the OE pads from honda came with 6 shims, 2 silver and 4 black. How do the silver ones sit on the pads? Over the black or what?

 

The silver ones face the piston.
So, over the black on the inner pad facing the piston.
IIRC you can also tell by the way the retainer clips are, it really only fits one way.