The default setting for PreserveMarkColors is True in the DefaultUser.properties file.
This means that the color separations for your job include all the colors from your artwork and colors from your marks. For example, if you have only cyan artwork and bring in a mark that contains magenta, yellow, and a spot color, and if PreserveMarkColors is set to True, the color separations in your job will be cyan, magenta, yellow, and the spot color. (If PreserveMarkColors is set to False for this example, the color separation for this job would only be set to cyan.)