The exact details depend on the binary system in question. Usually binary systems are derived from wild plasmids or viruses where one or more of the genes essential for replication, packaging or expression have been removed and transferred into a helper plasmid. This means you will have your main plasmid which will usually have a MCS which you can clone into like any other plasmid. This usually involves restriction digest/ligation or homologous recombination or recombinase mediated assembly. The main plasmid is then cloned and quality controlled by PCR and/or sequencing. You then need to transfect both your plasmid and the associated helper plasmid into the destination vector.