apologies if this is considered a necro: If you aren't going to use MO2, remove MO2's ini from (all) F4SE folders and the data folder to make sure they aren't being read or able to cause issues later. (back them up if you intend to use them again) The main advantage of MO2 is loose file management and having different load orders (and Fallout4Custom.ini) for different characters without installing everything over again. There are no advantages of using other managers other than to by-passing the clunky nature of the in-game manager. But if the load order is not large, in game mod manager works fine (and it's quicker to use with a gamepad instead of mouse). You just have to make sure all mods you've added to your data folder have fallout4.esm as a master file or the in-game will force it to the bottom of the load order, which is probably something other managers should do. All files should have fallout4.esm as a master. Had an issue with MO2 after I installed an update incorrectly (forgot to unblock the exe and Windows 10 and Windows Defender basically ate it; had to redownload, reinstall, unblock, disable Defender entirely and rely solely on a different antivirus). However, I like manually managing the data folder (cuz control freak) and only using Wrye Bash to flip-flop plugins as needed - with the exception of having to pack all the loose files into BA2 files. Where the real chore lies. Not really sure what the deal is with people offering developer/loose files but with no developer/source scripts instead of the real mod files that are packed properly so they don't load out of order and/or slow fps to a crawl. Got really irritating to manage all of them which is why I was using MO2: Loose file containment so I could pack everything. With Skyrim and SkyrimSE, (most) everything is archived properly, loads like it should, and is easier to work with in the data folder. There's just a lot of patches to manage. edit: not sure why a sentence was duplicated?