Is jQuery/Javascript Override-able using this theme?

Using free themes, are certain portions of the site simply inaccessible or disallowed to be overridden? I am finding limitations in various desired creative changes and am curious if there is a work around? Put plainly, do I have to start from php scratch to do what I want with a site, or can I identify and alter the pertinent areas of this site to accommodate style changes, whether minimal or advanced? This is a follow-up to an opacity question I prompted last week. I would like to make the Main nav drop-down pages reflect opacity, but it doesn’t seem possible. Is it possible, and if so, how?

Thanks in advance.