Using Webassist Framework Builder in conjunction with Bootstrap 3

I am in the process of updating an existing (framework) site, making it responsive, and using Bootstrap 3 in the css design process.

One issue I am having is implementing the framework plugins, and not duplicating the included javascript files.

When inserting a plugin to a framework page, the wizard adds code above the doctype declaration, to the head and MainContent areas by default.

If I delete the code inserted to the head, I tend not to have an issue with duplication of js files, but I wondered if this is likely to cause me other issues, and if not is there a file I could manipulate so that when the wizard runs, it doesn’t add the include into the head section.

I wondered if other developers are facing similar problems, and how they are dealing with them