Typically, you'll be using X Windows to get things done, but X Windows ultimately relies on Unix to accomplish anything: it "sits on top" of Unix. A basic understanding of Unix is essential to using X Windows effectively.
For example, you may need to provide an input file in some format (e.g. a programming language), and there will be no direct way of "writing" it. This means you need a text editor: a kind of word processor for "raw text".
Are you finding that after a couple of months you have 300 files sitting in your home directory? That can make things confusing. Learn about how you can organize your files in separate directories.
It's a fact of life in X Windows that not everything can be done by clicking the mouse on an icon. Sooner or later, everybody has to learn the basics of how to enter Unix commands by typing, using a command line interface. There is quite a lot to know if you want to become really proficient in Unix, but don't let that scare you! Learning enough of the basics to start your favourite applications is easy.