there is a way to add xchat icon in the Unity top panel, so when you hit X it minimizes there. By default it will disappear and you will not be able to activate it.
Launch "dconf-editor" , navigate to desktop.unity.panel in tree edit "systray-whitelist" to put 'xchat' to list.
you also need integration with Unity : sudo apt-get install xchat-indicator
To have notifications: do right click on channel, menu "Extra Allerts", and select all sub menus ("Beep on message", "Blink Tray Icon", "Blink Task Bar"). You will see blinking messages at icon that you allowed in dconf-editor.
Hint: to rejoin to few channel on startup, you need to join that channel and then in left tree of channels by means of right click add them to Favorite.