There are two folders that contain the CONFIGS for FH, to control what is backed up or is skipped. They are both in the root of the FH repository. One is on the main hard drive to be backed up, which is partially there to store the files until your external file history drive is reattached. The file that is on your backup, is updated whenever a backup occurs, (default 1 hour).
Although you can edit this, (which is what I generally do), the easiest method is to add or delete folders to or from "the library" file element, using "Explorer", or "File Explorer" as they now call it. (You can turn "viewing libraries" back on, (using Explorer I believe). FH works by automatically choosing all files and folders, and backing up all libraries.