Put the js files in the html-template folder and include the js files in the index.template.html which is inside the html-template folder.But the contents of the folder will get overwritten if you change compiler settings.Make sure to take a backup of the js files before making any compiler changes and update the index.template.html after updating the compiler settings.
I prefer to maintain my web files in a separate project using the web development plugin in FB4 (Help -> Add New Software -> http://download.eclipse.org/releases/galileo/)
When my Flex project builds, I have an Ant script that copies the bin files to my web project where they will be ready to deploy.
I find the default html templates pretty much is only good for testing. Most SWFs are actually part of a larger site structure.
Anyways, this method could be over kill if you just have a simple set up. I find it works well for me though.