Scalar quantities=quantities which don't have direction
Energy does not have direction ie we never say energy is given in east direction or in west.
Negative energy simply means that energy of system will decrease by that much quantity. 
						

							
We never can accurately measure energy of any system. What we measure is actually the change in energy of the system. The change is what is positive or negative.  Energy by itself can never be negative as no object can be so completely stable that is has it has zero energy. If zero energy itself is not possible, negative energy has no possibility. Hence energy is scalar and always positive.
						

							
We know that energy is a type of work done so ,
       W = F . S 
(here F and S i.e. force and displacement are vector quantities , also it is a dot product )
      So, dot product of vector quantities is always scaler, that's why we write -
     W = FS cos(theta)
 
 
      
						

							
Electric Current also has a negative sign which indicates the flow, still current is a scalar.
 
Vectors have direction. But what separates them from scalars is that they are added by vector addition.
 
Scalars can have a negative sign in them too. But they will never be added according to the vector addition.