As for the colors you have to set the midi in to HSB in the controller editor and play around with the midi out values or just use the controller editor if you just want 1 or 2 colors per pad.
As for the the FX make sure the pad is set to button and then toggle. that may be the issue
Cool i will have to play around with this tonight. If i have already done most of my mapping in Traktor using controller manager can i just set the colors with Controller editor and continue using my mapping?