In order to swap the Ctrl and Caps Lock keys in X11, you can add the following line in Section “InputDevice” of file /etc/X11/xorg.conf:
Option “XkbOptions” “ctrl:swapcaps”
If you woud like to keep the Ctrl where it is and make Caps Lock act as a Ctrl also, you can add:
Option “XkbOptions” “ctrl:nocaps”