Try to think for a moment about the literal and figurative meanings of light and dark. In the story, the literal light people are the English, who have colonized this part of Africa. Because they are Caucasian, they are "light." The dark people are the natives of Africa, who, being black, are obviously darker-skinned people. Now, generally, at least in the Western world, light and dark are often used metaphorically to represent positive and negative attributes. For example, we will say that someone has a dark soul, meaning he or she is evil somehow, and we use sunshine to represent goodness or happiness. These metaphors of light and dark are powerful in Western society, and if you pay close attention, you will be able to read or hear dozens of them.
So, generally speaking, a novel that concerns light and dark is going to tend to use these figuratively to represent some kind of goodness and evil or happiness and unhappiness. However, in The Heart of Darkness, this concept is flipped. It is the white people who are the bad guys, and it is the black people who are victimized by the white people. If you read the story carefully, you will see that many of the "white" or "light" images are attached to the English, who pretty much raped Africa, as did any number of other colonial powers. The images of the black people, while dark in nature, are about the darkness of what the English did, not about any figurative darkness of the natives themselves.
As to the difference between "dark" and "darkness," my thinking is that it depends entirely on how these words are used. I would say that "darkness" in this context refers to the darkness in the hearts and minds of the English, while "dark" is merely a descriptive term, which characterized the color of the victims of the colonizers.