If the water came from a municipal water supply, it contains chemicals necessary to prevent organism growth in the water. It is probably better to keep the tank full to minimize the amount of oxygen in the tank which can promote growth on the sidewalls. If it is filled with well water, or water of an unknown source, than drain it if you cannot fill it with water from a municipal source.
If you have municipal water available you can drain and fill it every few months if you are concerned about odors.