Make top-level folders for My Documentaries, My Movies, and My Series. To add "My" in front of the collection types has the advantage that all collections are beside each other on the hard disk, even if you put other stuff on there. "My" could be also replaced with your nickname or similar. Put movies, series, and documentaries in their own top-level folders. A good idea is also to make a My Garbage folder and put all movies in there which you probably will delete, but you are not sure for now because maybe some other people like them. If you later run out of space and need more to put on new stuff, you just have to delete the files in My Garbage without thinking too much what to delete during that stressful time. You can make a folder structure on lower levels as you like and there is no limit to the number of sub-folders you can make.
To avoid distributing stuff with bad quality or stuff which is simply not good, I recommend that you delete real crap immediately since probably nobody wants to have it anyway.
If you have more than one hard disk, implement the same structure on every hard disk. That way, if one of your hard disks dies, you lose only a part of each collection, but not a complete collection. Then there is also no need to move stuff around all the time and if a hard disk is full you just buy a new one and put your stuff on there. If you have an old hard disk, or a hard disk, which seems to be breaking down soon, you could put all the stuff on there, which you like least or with just acceptable quality. If the sick hard disk then breaks down the average quality of your collections, will immediately improve a lot...
If you have a messed up folder structure where video files and other files (poster, torrent files...) are mixed together you can move out important files (video and subtitles) with MFM. MFM does not touch other files so that you can review if there is any important file left in the messed up "empty" folder structure. Check the file names before moving the files, because sometimes files in folders are not named according to the content. If you drop the top level folder into MFM you can see the list of all files and scan that one for strange names. If nothing important is left just delete the whole folder structure.
If you have multiple files for the same movie, like cd1 and cd2, then they should be combined using AVI Mux GUI. If the files are still in the DVD structure you can use MakeMKV to convert them to a single video file. Both programs are more or less as fast as if the movie is just copied. The limit is how fast your computer can read and write to the hard disks. To speed up the processing it is better to convert the files from one hard disk to another.
To make the comparison as easy as possible some basic naming guidelines should be followed. FileBot is good to get the correct names from internet databases and rename your movies and series. If the names are that strange that FileBot cannot find them on the internet File Renamer Basic can be used to fix them so that FileBot can find them and make them 100% correct. If you share your collection with your friends it is important to have the same names for the same stuff, otherwise, they will be treated as different videos by MFM.