All files you add to the Baggage Files section are automatically included/exported in your HTML-based output. This is the best way to include files referenced in manually-edited code in your projects. You can reference all files in the Baggage section directly in your code. You don't have to add any path information because the files are always available on the same directory level as the other help files. All necessary copying and references are handled automatically by Help+Manual. (This is why Help+Manual uses a flat-file model without sub-folders in its CHM and WebHelp output, by the way: easier referencing in your code.)
You can use Baggage files for files referenced in the code entered with Insert > HTML Code, the HTML code editing function of the Insert Video Tool, all the HTML editing functions for HTML templates and the code you enter in scripts and macros.