What does it mean if the doctor says that only 5% of my heart is working?

Ejection Fraction. The ejection fraction (ef) refers to the percentage of blood that is squeezed out with every heartbeat. For instance, if the heart is filled with 100 ml of blood at the start of a heartbeat, and squeezes out 20 ml, the ef is 20%. Normal ef is 55-70%. You would need to clarify with your doctor if he means that your ef is 5%, or if he is referring to some other assessment/approximation.
Ejection fraction. The percentage usually refers to the amount of blood ejected by the ventricle or pumping chamber of the heart with each beat. The normal amount is 50+%. 5% is quite low and would be consistent with congestive heart failure.
Efficiency. Like any man-made machine, the heart is an efficiency rating. The normal is roughly anywhere between 55-65%. This is referred to as the systolic ejection fraction, or ef. Some people may be at 70%. Your heart function is depressed starting around 45%. At 5%, your heart is significantly weak and means that only 5% of the heart contracts to expel blood to the body.