How to use breakpoints in Eclipse
To put breakpoints in your code, double click in the left margin on the line you want execution to stop on. You may alternatively put your cursor in this line and then press Shift+Ctrl+B.
To control execution use the Step Into, Step Over and Step Return buttons. They have the shortcuts F5, F6 and F7 respectively.
To allow execution to continue normally or until it hits the next breakpoint, hit the Resume button or F8.
Put breakpoints - double click on the margin. Run > Debug > Yes (if dialog appears), then use commands from Run menu or shortcuts - F5, F6, F7, F8.
Here is a video about Debugging with eclipse.
For more details read this page.
Instead of Debugging as Java program, use Debug as Android Application
May help new comers.