The Preferences allow you to change the behaviour and the look of your current Ulysses project. If you want to adjust the behaviour, you need to go to the Preferences dialog. To change the look of the project, open up Fonts & Colors. Both can be found in the application menu. The subsections of these parts offer quite a lot of adjustable parameters, so you can modify it as you like and suite it exactly to your needs.
Whenever you change a setting in the preferences, it will immediately be applied to your current project. No restart, not even a save button.

In Startup, you can set some default settings when Ulysses launches or when you close a project. This allows you to get up and running ever faster. In Updates, you can enable or disable the automatic check for updates. You need an active Internet connection to do that.

Saving and Backup are both very important when it comes to getting your documents written to hard disk. By default, Ulysses auto-saves the whole project permanently. Apart from that, backup copies of your project are also created automatically.

The section Document Defaults allows you to set standard values, which are then applied to each new document. Counting lets you change the behavior of Ulysses’ counting feature.

In Standard Mode, you can adjust the behaviour of the Editor. One really interesting option is Typewriter Scrolling: it makes the currently active line stay in the vertical middle of the editor window. You can disable it for individual documents by Ctrl-clicking in the editor window and clicking "Typewriter Scrolling" in the Activate item.
The Info Panel section offers you some options to show or hide items of the Document Info Panel. By default, they're all enabled, but if you don't need this or that info, just disable it here.

In Console Mode and HUD you can adjust some settings for the Console Mode. Most of these settings are identical to the Standard Mode. One noteworthy exception is "Immersion". When this option is activated, the Console Mode remains active even when you switch back and forth between programs. The HUD displays you some document information while you're in the Console Mode.

The last three sections Paragraph Styles, Inline Styles and Markers give you lists of predefined Styles and Markers to which you can add your own.

Fonts & Colors

Font & Colors

The previous settings were primarily used for setting the behaviour of your project. In Fonts & Colors, you can adjust the look of the user interface, the Console Mode and printouts, so Ulysses can look exactly the way you want it. Ulysses also brings some default themes. You can set them with the drop-down menu on the top. You can import themes from other projects by selecting it in "From Project" in the drop-down menu. Again, any setting will be applied immediately.