We propose a query processing method for amalgamated knowledge bases. Our query processing method is an extension of the magic sets technique for query processing in amalgamated knowledge bases, augmented with the capabilities of handling amalgamated atoms. Through rewriting rules in a given amalgamated knowledge base, our method offers the advantages associated with top-down as well as bottom-up evaluation. We discuss how to handle amalgamated atoms, consider how to check whether an amalgamated atom is satisfiable in a fact set and how to extend a fact set by inserting an amalgamated atom. We also give the transformation procedures for amalgamated knowledge databases and show the correctness of our method.