Hello,

With the default config your arduino code can send serial text messages during debug. These message will display in the Serial Monitor. This is called shared USB mode. In this mode you can also send messages to the Arduino from the Serial Monitor.

Alternatively you can set the debugger to use different hardware serial port if available with the board you are using. See project properties called RemoteTransport, RemotePort and LocalPort

Or the debugger can use SoftwareSerial on any two digital pins if you have something like an FTDI cable. RemoteTransport, RemoteTx, RemoteTx and LocalPort

The latter parts of this video describes some of this http://www.youtube.com/watch?v=fFM8_RhIG0U

This wiki article also describes some of this http://www.visualmicro.com/post/2012/05/06/Configure-debug-for-other-types-of-se...

Also you can see the tool tip help below each project property for more info.