Most APIs have an asynchronous option which is better since it improves loading times - you can dynamically create a script in your plugin's startup code and usually it then makes a callback to say it's loaded. That's what the Facebook plugin does, it loads Facebook's script dynamically without adding any script tag to the HTML page.
However if you're stuck with an API that doesn't support that, there's an undocumented feature that lets you do that - add a dependency property to GetPluginSettings() in edittime.js like this:
This will then add a script tag for "myfile.js" in the HTML and copy myfile.js from your plugin's folder to the exported directory. However, I would reiterate that using APIs asynchronously is better. Which API is it, out of curiosity?