You can create breakpoints in the source editor by double clicking in the gray column on the left hand side of the editor window. In this context, you may find it useful to add line-numbers to the source view by selecting Window -> Preferences, expanding the node General -> Editors -> Text Editors and selecting "Show line numbers."
Also note that you can create breakpoints in this fashion before beginning your debug session. You may also switch back and forth between the Debug and Ada perspectives at anytime by clicking on the "Ada" and "Debug" buttons in the top right-hand corner of the display.