Most of the customization is done through the wiki itself, by editing the wiki pages. Some of the customizations have to be enabled in the configuration first, though.
You can upload your own logo image as logo.png, this will make the wiki display it on every page next to the title. You can also change the logo_page configuration setting to use a different page.
You can provide your own stylesheet (CSS) for the looks of the wiki, just put it on the page style.css. If you don't want people to mess with it, you might want to lock it, see below. If you want to use a different name for it, change the style_page configuration setting.
The content of the main menu can be defined on the Menu page. Hatta simply takes all the links that appear there, and displays them as menu on top of each page, in the order they are defined. External links are ignored for security reasons. If you want to use a different page for the menu, change the menu_page configuration setting.
The Locked page contains a list of pages that are not editable through the wiki. You can use it to lock the above pages. Note that to lock the page itself, you have to edit the corresponding file with a text editor and commit the change. Change the locked_page configuration setting to use a different page.
Note: Since hatta 1.3.0 you can also disable editing of the whole wiki in the Script settings, by setting the read_only configuration setting.
Since hatta 1.3.3 you can customize the smileys and other images displayed by your wiki. Just set the icon_page configuration setting to some page name, for example Icons, and put links to images or images themselves on that page, with link text indicating the symbols to use for them. You may want to lock that page to prevent silly pranks.
Note: For security reasons, the page will become read-only then. You can edit the file or temporarily remove the option to edit it.
Since hatta 1.6.0 you can show any text on the editor page, simply by putting it on the Help page, or any other page set by the help_page configuration option.
Since 1.5.0 page templates are supported, via Jinja2. For example, a copyright notice can be added to the layout template and it will be displayed on all pages. However, any changes to the templates are going to be overwritten on upgrade. Hopefully future versions of Hatta will have theme support to modify the templates more gracefully.