Include both in script tags in the header of your page:

<script src="cytoscape.js"></script>
<script src="JSmol.min.js"></script>

In your HTML, use a div element for the jsmol content and another for the cytoscape content. See here for cytoscape and here for a simple JSmol example or here for a more complex one or look at examples in the jsmol.zip archive in the Jmol distribution.