If you don't have your folder organised you're asking for trouble. It's extremely difficult to update mods in a messy folder but so easy to handle it if you have things organised. It's so much easier to go through organised mod folders and look up each mod to update than it is to have to crawl through piles of mods in a single unorganised folder that you've forgotten you even have...that's asking for a broken game and a corrupted save file.
My folder is organised mostly as CAS/Build and then game Mods. If I have a problem in my game I can immediately remove all my mods to ensure it doesn't happen without mods, then add all my CAS/build stuff back in to verify it's not that (which most of the time it's not that). Then I can slowly folder by folder add the other mods in until I find the problem folder or folders. Then it's a matter of adding mods in those folders back one at a time until I find the culprits. It's much more targeted than doing half of my mods folder at a time and guessing my way through piles to find problems. I had an error yesterday that was telling me it was about careers but I have no custom careers. It turned out it was a faster writing mod, it took me 1 folder to find the issue and literally it was the first mod I added back so it was 2 game loads. If I 50/50'd the entire folder it would have been dozens of game loads before I found that one mod causing this error.
Here's how I organise mine if anyone's interested: https://imgur.com/a/KscKhsv
I do have 2 folders for mod authors specifically, Bienchen and LMS and that's because it's just easier when I download a tonne from them and I only put LMS's small mods into that folder because they come in a pack so it's easier to update them there - I put all her other mods into the other folders. It's much easier to find the dress or lipstick or tattoo or floor covering or feature or tweak I'm looking for when it's all in an expected place.
When it comes to tweaks/hacks and new features it's easy to know what's what as well. If it's an existing feature that's been changed it's a tweak (like changing all beds to be same quality, or whim/pregnacy etc overhauls) . If it's a new ability based on an old feature it's probably a hack (or that's what I call it: examples include teens going to uni if they max out their grades, bugfixes, adding stuff to be buyable from pc, overhauls). If it's something new added in it's a new feature (like MCCC, Slice of Life, Better Schools, new spells, transfer inventory, hirable dog walker).
I further split things up/out of tweaks and hacks into other folders like Speed Ups (faster writing, painting, fishing) and my retail mods as well because they get lost in the tweaks folders as I have so many. If I notice a theme in my tweaks folder I make a sub folder to separate it out. Just after uploading pics I added a tweak mod that gave all bars the same quality so I moved the bed one and the bar one into a new folder called "Tweaks Quality Overhauls" and now I don't have to scroll through so much in my tweaks folder. Before I had MCCC I had an autonomy folder but now I have MCCC I don't need ANY autonomy mods so that's fabulous and saves me a LOT of time!
I've never used a mod organiser. To be honest I don't trust them. But you have got to have some form of organisation because just dumping files into the mods folder is the worst idea ever. Just remember you can't put script files in too deep a folder. I have a rule mine are no more than 1 down so many of mine are in the base folder as you can see.
