I would definitely use the black thinner pads for the mem and vrm areas... they seem to be better at conducting heat, not just because they are thinner but they are more "gummy" and likely make a better seal on both sides (block and chip). Seems like from all the videos and write-ups I read the dark pads were used... I only used the other pads in 2 spots on each block because some of my chokes were clearly not making contact with the dark pads.. all of the other components made excellent contact with them.
another note on the white/pink pads.. they only have one side that peels off, the side that is pink is like a heat conducting fabric and it does not come off. I put that side against the choke tops and the sticky side on the blocks.
edit: here's a pic showing the two spots I used the other pads on.. the deepest recessed areas on the blocks. this will obviously be different on a 480 block
http://i36.photobucket.com/albums/e4...G/P1020147.jpg