Here's the situation: you have stored years worth of backups and copies of your working folders. So far so good. But unfortunately you are not very systematic so you've created a mess. Some things are missing and other things have three or more copies of the same file!
But there are two useful things BC can do for you.
Look closely at a pair of folders in the tree
Using your mouse, drag both directories onto the BC window. Hit the expand button. Whoa, these backup files on the right are a mess. The files are named "a" through "i"
If we want to examine foo and bar, we rightclick them and choose set as base folder.
Flatten the entire tree, ignoring folders, showing all files
This option shows all the files, no matter how deeply buried. You can sort the flattened tree by date, size, and rightclick each file for a context menu. The screenshot here tells us four things:
the equals signs in the middle, with the 0111 symbol are telling us that byte for byte, the contents are identical in this pair of files
the directory on the right has doubles of almost everything
the directory on the left has no copies of file "i".
the path of each file is listed
Unfortunately, this is the end of the road. Beyond Compare is the wrong tool for thoroughly dealing with redundant files. If you want to methodically solve redundancy issues in backups that you have already made, search online for duplicate file finder software.