I was confused by overlapping topics as well, but playing around with it I found a couple of ways to minimize that. One is to close all the main topics that you are not currently using (just tap the end of the branch line and the topic will close/open). In the menu selection "tools" you can select "eagles eye view" to see the whole map, but you can't manipulate it, only highlight the area you want to view closer, then click "okay".
Another way to minimize overlap while you're working on the whole map, is to drag the lines for the main topics out farther, alternately, so when they are open they will not overlap too badly.
You can also isolate each main topic and its children by pressing the stylus on the topic and selecting "promote to map". That makes a separate view, in its own window, of the topic and its children, with a little red arrow beside the topic name, which, if you click, will return you to the main map. This adds to the size of the entire file, but for complex maps it is a real help. I agree, overlapping topics is is one way that Pocket Mindmap is inferior to the parent PC program, and I do hope they design a nice automatic solution for it in the next version.
Bishops Mills Natural History Centre