You must determine the center of gravity with all the weight including batteries. if your IMU is dead center then all you need to worry about is the z position whether this is higher or lower than the IMU if all at the level of the IMU then cool.. If not you must enter a minus figure for lower it is very rare it would be a whole number. Google COG Wookong and you should see a video on how to determine COG.
PS If you have landing gear the COG will more likely be a little bit lower..