Second screen mirror one desktop
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I am assuming you are using an app such as Duet Display or Air Display for this purpose. It sounds like you are attempting to extend your desktop, rather than mirror a desktop. You will need to go to System Preferences -> Display -> Arrangement. From there, you can shoes to extend the Desktop. 

Following these steps, you will be able to have one or more windows open on your iPad screen, and several desktops on your Mac screen as well.