If i recall correctly, the Audioengines's are rear ported so you may want to move them away from a wall to prevent bass buildup. Inherently, the audioengines may just be designed to have a bass hump and there may be nothing you can do about that, although i've not heard of the audioengines myself. Alternatively, you may choose to move yourself off-axis such that the tweeter is facing below your ear.
If you are not certain that the woofer is bouncing lower frequencies off your desk and into your ear you can check this by putting some carpet/dampening material on your desk and see if the reflections still occur.
If you are simply wanted to decouple your speakers from your desk, I recommend Primacoustic Recoil Stabiliser (be sure to get the right size).
Lastly, your room and speaker placement may just be bad. Consider using bass traps to treat your room, if serious.











