Why wouldn't you give us your context? It would be much easier to answer your question, because the terms look like ones from some special field of knowledge.
The only thing I can suggest is that it refers to literature analysis, I mean a story/novel etc. can have a primary conflict, that is the key idea of the book, or realtionship between the protagonists or something like that. A secondary conflict is minor events and ideas, which are observed against the background of the primary conflict and are important as well. I may be not quite accurate in my explanations, this is just all I can remember at the moment. I hope it helps.