Much love for StackOverflow. You definitely need to make use of that site.
As for your specific question, you are going to have to modify the index.html file that Construct generates to integrate your js file into the overall page load. Otherwise, it doesn't know where you are asking it to go. By extension, this also means that calling js functions with the Browser object will NOT work in preview mode, since Construct knows nothing about the extra js file or the include that you have included manually in the published version.