Currently Duet is preventing the iPad from being the main display due to outstanding issues with OS X when Duet is the primary monitor. We've submitted bug reports and are awaiting responses from the developers team. If this is a critical feature for you please email us at firstname.lastname@example.org and explain your use case so we can look into any workarounds.
You can change your primary monitor settings by opening System Preferences > Displays > Arrangement. Then click and drag the small white menu bar to your preferred display. OS X will remember this setting for your display configuration.
If you'd just like to change where the dock is for the time being, you can move your cursor to the bottom of any display and the dock will move to that display. This setting is not remembered by OS X and you will have to do it every time.