Custom Theme Pagination

I would like to use your plugin in a custom theme that makes use of different post types. I’m having difficulty understanding how to to edit the $query from the description in the FAQ section. Would you be able to point me to the correct way to enable the plugin.

The custom post type is job.
The loop file is loop-seeker_nofeatured.php
This is the index page code:

<?php
						$have_posts = false;
						$posts = query_posts( array(
							'post_type' => 'job',
							'meta_key' => 'tgt_featured_job',
							'meta_value' => 'yes'
						) );
						if ( have_posts() )
						{
							$have_posts = true;
						?>
							<div class="box_text">
								<div class="jobs">
									<div class="latest_header_sub2"><?php _e('Featured Jobs','jobpress');?></div>
									<p>
										<?php
											//echo $jobtype_links;
										?>
									</p>
								</div>
								<?php get_template_part('loop', 'seeker_featured');?>
							</div>

Pagination :
<?php get_template_part('loop', 'seeker_nofeatured');?>

Any help would be much apreciated.

http://wordpress.org/extend/plugins/ajax-pagination/