There are many ways in which you can add a line breakpoint. The simplest way to set a breakpoint is by clicking on the breakpoint vertical strip next to the source line where you want the breakpoint to be. Another way to set a line breakpoint is to move the source viewer's text caret to the line where you want the breakpoint to be and then selecting Breakpoint | Insert Breakpoint or by selecting Insert Breakpoint from the popup menu that appears when you right click on the source pane. Breakpoints can be set even when a debug session is running.
Another way to set a line breakpoint is select Breakpoint | Add Breakpoint | Line Breakpoint. When you use this method of setting a breakpoint note that the View Code feature of the Breakpoints dialog that lists all breakpoints for the current project will be disabled when you select this breakpoint because when using this method of adding a line breakpoint, no source file is associated with this line breakpoint whereas if you use the first method of clicking on the breakpoint strip BugSeeker knows which source file you are setting the line breakpoint.
Whichever method you choose to set your line breakpoints is up to you. When BugSeeker goes about registering these breakpoints when a debug session starts it only cares about the class name and line number where the line breakpoint is to be set; any information about the original source file will not be used nor is needed. Thus, sometimes when you open different versions of the same source file you will see a breakpoint icon in the file even though you did not explicitly set the breakpoint in that particular file.
If you attempt to set line breakpoint on the same line and class as another line breakpoint, a warning message will be displayed and you be prevented from adding this duplicate breakpoint.