When you start programming your first web app you are doing something that you have never done before. It's a new challenge, a new opportunity, and in the case of software development, something so specific that it's probably never been done before.
Confusion, therefore, is a sign that you are heading in the right direction. It's a signal that you have engaged in the problem solving pursuit that is math and technology and that it's time for you to dig deeper and keep going because clarity awaits.
Read and review class materials and videos multiple times and the information will eventually make sense.