The color red is only mentioned three times; in reference to the "red men" (Native Americans), in describing Old Scratch's belt or sash, and in describing his eyes.
This limited application makes it difficult to connect it to a clear symbolism. Red is often associated with blood, violence, and anger or passion, although in the context it might also represent the fires of Hell, and the Devil's more common representation as being red-skinned. If a connection was intended by the author, it may be that the "red men" were more savage and therefore more in keeping with the Devil's preferences, particularly through the human sacrifices he mentions. The red in his eyes and sash may also be simple references to his true nature.
The color black appears a bit more frequently; the swamp is described as black, as are the trees and the mud inside it, as well as some mold that Tom pokes at in the old Indian fort. The ending of the story is also heralded by the appearance of a black thunderstorm. Of course, most significantly, Old Scratch is black, and is referred to as "the black man" more frequently than by any other title.
Black typically is associated with night, evil, death and decay. The blackness of the swamp clearly associates it with decay, and possibly with evil because of its haunted reputation and the fact that Scratch lives there. The blackness of Scratch's body and hair might represent that he is an embodiment of evil or death, or simply as a means of communicating his supernatural properties.