The Drupal Forms API comes with some powerful features, including checkboxes which allows a bunch of checkbox options to be grouped together. Included in this functionality is the ability to set default values, i.e. set your chosen boxes to be on.
However, it is not immediately obvious how to programmatically set the default values using the '#default_value' key. The key expects an array, so I tried the usual contenders such as an array of 0s, 1s, 'on', FALSE, TRUE etc etc and just couldn't get it to work correctly.