CodeLite IDE

Currently a separate console is opened for the output which goes to a console. This works with the following settings in
Settings -> Preferences -> Terminal:

/usr/lib/codelite/codelite_xterm '$(TITLE)' '$(CMD)'

How can I configure it that the output goes to the built-in output pane ?

You cant.
However, you should really read the "how to post" thread (see my signature) as many changes have been made in that read (terminal handling by CodeLite)
in later versions of CodeLite, you just pick the terminal you use (QTerminal, Mate, Konsole, gnome-terminal etc)