ClickLess has two Menu items for this purpose:

Options...Always ClickLess this Program

When you click on this one, the program selected on the Tree View and shown on the bottom left side of the Status Bar will be registered to be monitored forever. So if you don't select this program again it will be automatically monitored, allowing you to work with multiple registered programs without worrying about which one is selected.

Options...Edit Registered Programs

Use this menu item when you want to unregister a program. A dialog box will be opened.

It will show the list of ClickLess' registered programs. Just click on the one you want to unregister and click the Delete button. In case you change your mind, you can register the program again using Always ClickLess this Program, described above.