From your Coot window, you can go to Edit->Preferences, then select the "Map Colours" tab in the resulting window.  You should see radio buttons for "Coot colours" and "O colours".  The way these work is that you select the desired colo(u)r for the positive difference density (e.g. green).  The negative contour is then 120 degrees ahead (clockwise) on the color wheel if you choose Coot colors, or 120 degrees behind if you choose O colors.

It looks to me like you want positive to be green, and negative to be red.  So I think you want Coot colors, and positive set to green.  At the moment, it appears that you have O colors.

I have no idea if your selections will be kept the next time Phenix opens a window for you.  Probably not.