Is there a recommended method to construct a form on a grid (2-dimensional array) with Form API?
If you need a table and put checkboxes on the left you could use http://heine.familiedeelstra.com/new-tableselect-form-element-in-core

Alternative you could theme your form. Therefore you have to write a theme_form_id which
drupal_render the elements and put them together with theme('table').

PS: This will perhaps land in drupal8: http://drupal.org/node/80855