Work is the integral of F dot dr. That's the definition, plain and simple. What the dot product means is that the answer is the scalar magnitude of the force vector F projected along the length vector r. Because of this definition, the work done becomes a vector with one dimension of direction, + or -. So we make the important distinction that Energy is a scalar while Work is a vector. I just finished my AP Physics class not 3 months ago, so this is pretty fresh in memory. Work can either add or subtract from KE, PE, etc. In the case of a repulsive force, negative work is done, decreasing the KE and increasing PE. I believe what you're thinking of is the direction in which KE(Kinetic Energy) or the like is changing. If the electron is "climbing" a potential spike, then work done subtracts from KE, and if the electron is "falling" into a well, then the opposite is true. The justification is the definition of work and the nature of the force.
Also related is momentum, which is a vector quantity, and may be more what you're looking for. Momentum is the product of the scalar mass and vector velocity, which yields a second vector representing momentum. Force acting over time changes momentum.