This plugin inserts pagination to your blog, archives and search results based on logarithmic calculation for a more evenly distributed link-juice.
Yes, it does. It uses internal WordPress functions to generate the links so all changes to your link structure within your WordPress site will be repsected.
Until i find a better solution you will have to use the template-tag
<?php the_wp_lopa('pages_below'); ?> to call the pagination element. Make sure to uncheck the places on the Settings page aswell.