A Prezi is slightly different than any other presentation, in that it's mapped out on one page. The most important tip for creating Prezi is to structure it in a way that makes sense as a whole picture. Zoomed all the way out, it should be like a floorplan of what you are trying to present.
Start with the main points the presentation needs to make. Within those main points, add details and images related to them. When zoomed out, the Prezi should look like a map to the conclusion your presentation is drawing. Use things like arrows as visual guides to keep the audience thinking about how each "slide" is connected to the next one, as well as the overall topic.
Another tip is to not add too many levels of detail, or don't zoom in too much. Getting too in-depth with any one subject will lose the audience's attention. Don't lose focus of the main path the presentation is following. On a related note, zoom out every once in a while to provide context as to where the current slide is in relation to the whole idea.
One interesting feature of a Prezi is that the screen can spin in different directions when zooming in and out. Avoid doing this too often, as it can make the audience dizzy.