FacetWP comes with many filters which gives you the power to mould it to your needs. Generally, you would code these filters into your child theme in the functions.php file. This has drawbacks, however. If you do not use a child theme or you change to a new theme, you stand to loose functionality on updates.
FacetWP Manipulator allows you to add code to specific filters to manipulate functionality without hard coding it to the themes files. This means that your functionality via filters can be activated or deactivated without touching the file system.