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$jinput = JFactory::getApplication()->input;
$array['three'] = $jinput->getArray(array('one' => '', 'two' => ''));

if (is_array($array['three']))
{
// implode array to convert it into string (persist)
$array['three'] = implode("|", $array['three']);
}
else
{
// explode string to convert it into array (render)
$exploded_array = explode("|", $array['three']);
$array['one'] = $exploded_array[0];
$array['two'] = $exploded_array[1];
}