Printing a term using custom formatter
if you want apply specific display formatter to some field like taxonomy terms, the best way is to write a display formatter module, and apply it to your entity_type via display setting on specific view mode, so if you want do this completely programmatically you need:


write display formatter moule
define view mode if necessary (e.g. for node we have full, teaser and ...)
add configuration to field instance setting


if you need some sample code to write display formatter module, let me know...

EDIT: if you want pass field instance setting to field_view_field you have something like this:

$display = array(
    'label' =&gt; 'hidden',
    'type' =&gt; 'colorbox',
    'settings' =&gt; array(
        'colorbox_node_style' =&gt; 'simpledeal_company_medium',
    ),
);
field_view_field($entity_type, $entity, $field_name, $display, $langcode = NULL);


this example code is about colorbox display formatter, should be replaced by yours

to do above via admin you should go to vocabulary display setting admin/structure/taxonomy/VOCAB_NAME/display, in CUSTOM DISPLAY SETTINGS check Taxonomy term page and set your display formatter, in this way you may do not need to change taxonomy-term.tpl.php