The design of a website isn't simply 'what looks good'. A website is a series of interactions leading to a result: finding something out, buying an item, signing up to a newsletter.
As a result what is being designed is a system, a product or an application, so its design needs to arise from how these goals can be most easily acheived by users.
The website's final layout and the user's movement through the website are results of the design process, not just by-products of the 'look and feel'.
A website is more like a usable object than a flat brochure, even if marketing is the intended purpose.
As such care needs to be taken in designing 'how it works'. We've already looked at the informational structure of a website, this will suggest how someone might navigate through the site to achieve their goals. These goals are indicated by user and organisational research.
From this we can construct a wireframe prototype. I usually do this in HTML (being a web developer), but it could as easily be done using pen and sheets of paper.
Wireframes aren't, as some people believe, hierarchical 'family tree' style sitemaps. They are an interactive demonstration of what a site will do, not what it will look like or how it will work will work.
Each page shows the responsibility of a website page or control and what will happen in different situations, for example, on a form, what will happen if it is completed and submitted, or submitted incomplete.
People using a website are likely to become very easily visually confused. Each page needs to have attention paid to how user and site goals can be acheived through layout alone.
People have different visual fixation patterns depending on the content of a web page. Designing the layout of a page can focus users on achieving what they would like from a website.
One method of prototyping is to lay out a site using blank boxes, indicating the location of images, navigations and text.
Once you have designed what your website will do and how it will be layed out, you have a clear set of instructions for how the site will work. Before that takes place it is very much worth testing these prototypes with end-users.
The final design step is the look and feel of the site. It's important that a balance is maintained between the functionality of the site and its usability and the end look.