Let me describe for you an entire web design process with several sentences below. Generally it works for both – web sites and web applications.

• Drawing a sketch or concept (paper, whiteboard or any other surface)
• Creating a basic black and white wireframe (Visio or any wireframing tool)
• Designing a colorful high fidelity mock up (Photoshop, Illustrator, Axure, HTML)
• Developing a prototype (CSS, HTML)
• Responding to users feedback and updating design, delivering relevant screen designs to web developers