Well, the search unit for WPFTS is a wp_post record. It’s a post, page, custom post, or attachment.
In order for a PDF file to be searchable, you need to upload it to WP Media Library (you can find lots of free plugins that allow bulk file uploading to WP Media Library).
Another way is to include the PDF file as the custom meta field to another post.
Also, you can place a direct link to PDF into the post/page/custom_post content.
The basics of the plugin functionality are described here
https://fulltextsearch.org/documentation/
But the plugin is much flexible than it may be seen. Please explain your exact application and I will even send you the small addon file which links your data with the WPFTS Pro index (if required).