When ChartOverlay is already running and you click its icon, that normally just makes ChartOverlay the active program. If you check Allow Multiple Copies on the General tab in the Options dialog), you will be able to run additional copies of ChartOverlay, which means you can have multiple simultaneous overlay windows.
When you do this, the first copy you start will be the Primary Copy. Only the primary copy will have access to the Hot Key (to hide or show the overlay), and only the primary copy can save changes to your settings (via the Options dialog or the individual tool dialogs).
We recommend caution when using this feature so that you do not overload your CPU or use too much memory. Keeping each overlay window as small as possible should help.