If you have a script file, you have two primary options for adding it to your site:

• Host it externally (e.g. on your existing non-KK site) and use the Site Map Inspector's Scripts panel to add an external script reference.
• Import it as an internal script by opening the Scripts panel, clicking Import Script, and using the file browser to locate and select the file. A new internal script will be created with the same name as your file.

(I've attached images showing the interface elements needed to achieve these outcomes).

Whichever method you use, you can then use the Master Page -> Meta Tags -> Scripts tab to assign the resource to your master page and publish it.

If this doesn't work for some reason, please let me know.