Adding multiple fields in node_save()
Second index after 'und' is used for delta of values. You can make it 1 , 2, 3 etc to add multiple values... Something like below...

$node-&gt;field_my_custom_field['und'][0]['value'] = 'my value one';
$node-&gt;field_my_custom_field['und'][1]['value'] = 'my value two';
$node-&gt;field_my_custom_field['und'][2]['value'] = 'my value three';
$node-&gt;field_my_custom_field['und'][3]['value'] = 'my value four';