There are basically three levels of customization you can do with a kwiki site. They are discussed from easiest to hardest:
There are 2 directories in your kwiki installation that contain files that control the layout and appearance of your web pages:
You can change the html and css files anyway that suits you. It is generally best to copy the modified files into local/template and local/css. This way your changes will not be overwritten if you later do a kwiki-install --upgrade.