I have a few html and javascript programs that outline a webpage with a user-interactive tasks. The files work in PyBossa (http://pybossa.com/) but I want to incorporate them in my Drupal website. I am very new to Drupal and am not sure how to go about doing this.
Depending on what you need to do, you'll either want to expose it via a custom module or, more likely, through a theme. You'll need to specify your Drupal version and purpose for a better answer but, in general, you'll want to add the files to your theme_name.info file (for D7 and below) or theme_name.libraries.yml file in D8. You can also add it to your template.php (D7 and below) or you theme_name.theme file.
We need more info for your Drupal version and the specific use case. As you can see, there are many ways.