Line breakpoints are set on an executable line of a program.
1. In the editor area, open the file where you want to add the breakpoint.
2. Directly to the left of the line where you want to add the breakpoint, open the marker bar (vertical ruler) pop-up menu and select Toggle Breakpoint. You can also double-click on the marker bar next to the source code line. A new breakpoint marker appears on the marker bar, directly to the left of the line where you added the breakpoint.

Also, the new breakpoint appears in the Breakpoints View list.
While the breakpoint is enabled, thread execution suspends before that line of code is executed. The debugger selects the thread that has suspended and displays the thread's stack frames. The line where the breakpoint was set is highlighted in the editor in the Debug Perspective.
The Javascript debugger has a client/server design so that it can be used to debug programs that run remotely.
After you have finished editing and building your Android program, you can launch the program on your workstation using the Debug > Debug As > Xun Bug menu item on the workbench. Launching the program in this way will establish a connection between the debugger client and the Android program that you are launching. You may then use breakpoints, stepping, or expression evaluation to debug your program.

When a thread is suspended, the step controls can be used to step through the execution of the program line-by-line. If a breakpoint is encountered while performing a step operation, the execution will suspend at the breakpoint and the step operation is ended.

Select the Resume command to resume the execution of the currently suspended debug target.
When the Browser suspends a thread (due to hitting a breakpoint or stepping through code), you can evaluate expressions in the context of a stack frame.

1. Select the stack frame in which an evaluation is to be performed. The evaluation context will be the currently selected variable in the view. If no variable is selected, the selected stack frame will be the context.
2. Expressions can be entered and evaluated in the following areas: ◦ Display View
◦ Detail Pane (in the Expressions View and Variables View)
◦Javascript Editor when it is displaying source and it is not read-only
Note: Evaluations cannot be performed in threads that have been manually suspended.
I am using eclipse 3.6 and ADT 16.0.1,the Terminal is 2.3.3 or 4.0.3
The first version is simple and have no GUI to select Terminal
Please check this and when the console output
[2012-02-15 13:56:14 - HelloProject] ------------------------------
[2012-02-15 13:56:14 - HelloProject] Android Launch!
[2012-02-15 13:56:18 - HelloProject] Performing com.phonegap.example.PhoneGapExample activity launch
[2012-02-15 13:56:18 - HelloProject] Automatic Target Mode: using existing emulator 'emulator-5554' running compatible AVD 'test'
[2012-02-15 13:56:18 - HelloProject] Uploading HelloProject.apkdebug.apk onto device 'emulator-5554'
[2012-02-15 13:56:19 - HelloProject] Installing HelloProject.apkdebug.apk...
[2012-02-15 13:56:26 - HelloProject] Success!
[2012-02-15 13:56:26 - HelloProject] Starting activity com.phonegap.example.PhoneGapExample on device emulator-5554
[2012-02-15 13:56:28 - HelloProject] ActivityManager: Starting: Intent { act=android.intent.action.MAIN cat=[android.intent.category.LAUNCHER] cmp=com.phonegap.example/.PhoneGapExample }
then you can debug javascript