Can I do it like I can add a CSS file, so if I just copy the contents into a specially formatted card the .js will be usable by the site?
Not *yet*.
By Decko 1.0 we will add javascript mods api, and that will very much mirror the new stylesheet infrastructure.
At present, I think the only way to do this is to upload a js file as a File card and add an explicit javascript link to your head tag in your layout.
Okay. If uploading it as a file will get it on the server, then I should be able to play around and see if I can get anything to work.