To get started with the program, launch it, and a simple command window-type interface will appear. Quttera URL Scanner will complain that it's missing a CDB package, its database, but that's easily fixed: just type UPDATE, press Enter and it'll download and install the necessary components for you.
And with that done, you can now run a scan immediately. Simply type a command like scan www.google.com (using your own preferred domain and page of choice) and watch as the program downloads up to 10MB of content, scans for problems and displays any results.
Does it work? Yes, to an extent, but you do have to be careful how you interpret the results. We found the program would quite often report innocent pages as "potentially suspicious" for one reason or another, and you'll need some web development and security experience to properly understand its reports.
Still, if for instance you have your own website then you could use Quttera URL Scanner to check it on a regular basis, perhaps automated via a script. What you'd then be looking for would be any changes which might indicate you'd been hacked, and there the program could be very effective.