Topics are arranged by connectors. These remain invisible except when editing. Connectors define the progression of the presentation. If you move a topic, the connectors attached to it adjust automatically.
To change the order of topics, drag and drop using the left sidebar.
This will automatically re-adjust the topics and their connectors.
Animations can be added to sections or topics. There are two options: fading and zooming. They are designed to help focus the presentation for the audience. Fading brings a specific topic or text in and out of the presentation, while zooming focuses on a certain area of it.
To add fading to a topic, select the topic, right click and select "Add Animation." You can select fade in or fade out on the right side bar.
Once you've added animations, you can click on the "Animations" button on the context toolbar to see the animations overview. To re-order, drag and drop the animation on the sidebar. To delete animations, right click on the specific animation and select "remove animation."
Another animation feature is zooming, which allows you to focus the audience on one particular aspect of your presentation, such as a title or chart. To use this, select "add zoom area."
A blue box will appear on your presentation. Drag the corner to adjust the size and location to cover the area you want to add zoom to. These can be re-ordered and removed the same way as fading animations.
Prezi's video tutorial of animations here gives a good idea of how these features work in a presentation.