I agree with above it does kinda stick out there. If that the color theme you plan on going with that painting in would look good. I would paint the box first than the drawers. This would be keep box in unusable state for the least amount of time being you can always pull a drawer or 2 out here or there until you finish them all.
I've got the same situation - red tool box that sits on top of a black tool chest, dark grey cabinets. I'm in the process of garage redo and plan to install upper cabinets - paint the boxes the same dark grey with red doors. Maybe there is something else in the garage you could paint red that would balance it out and keep that pop of color
ASK THE TOOLS.. I've always figured if the tools don't complain then all is good. I always seem to have more important things to do than worry if I need to redecorate or my fung shuey is correct.