How do I use the Link Engine to open all links in the main Wavebox window.

Go to: Settings > Link Opening > Customize Link Open Rules (button)
Under the 'External links' section, click 'New Rule'
In the 'Match' field, click the advanced mode icon (up arrow) on the right-hand side and enter a * (asterix) in the text field.
Set the 'New tab action' to be 'Open as a tab'
Click 'Save'.