I would apply the "do I need this" mentality to each mod. Remember the author's system is quite a bit more powerful than yours.
Also remember that it is your game you are modding. There is a lot of personal choice involved (hence my opening statement about the excessive mod list). Hopefully this experience will teach you everything you need to know to mod how you want to.
none of my mods show up in the skyrim data folder, they all seem to be installed on MO but skyrim launcher shows nothing on the data folder and NMM says nothing is installed - i am launching through SKSE and it doesnt even say SKSE isnt installed but none of mods seem to load?
ENB doesn't load either and there are no errors but everything is there for the ENB?
whats happening? mods are stuck in other mods and I cant seem to get them out!
Alright to update after removing all mods from MO and reinstalling one, I can see that even though it has been ticked it is not in the DATA folder of my skyrim and so obviously does not activate.
Never used MO but I'm pretty sure it doesn't put the mods inside the Skyrim\Data folder. MO creates a separate folder structure and uses fancy shortcuts to trick Skyrim into thinking the mods are in the right place. It does this to keep the Skyrim folders vanilla. Look in the directory where MO is installed for the mods.
Trojan Horse, go to this thread, The Elder Scrolls V: Skyrim - MODS & TWEAKS, and follow the first post, at least through 1 to 5, those steps should always be done and you need SKSE, LOOT and TES5Edit to make sure all is in good order (or so is my understanding of it anyway). If you want more information about Mod Organizer I highly recommend Gopher's instructions on YouTube.
Might look a bit overwhelming but for me those YouTube clips was a godsend and made it much easier for me to understand it all.
But as Fanatic said, Mod Organizer creates a "ghost" folder where all the mods are and the Skyrim folder is never touched. If I would click directly on the Skyrim TESV.exe it would start the vanilla game without any mods. In my example all mods are located at E:/Games/Steam/SteamApps/common/Skyrim/Mod Organizer/mods
I think you can have the Mod Orginazer anywhere, I just put it in the Skyrim folder to make it easier for myself.
Hope this is of any help, if not I am sure others will come around with more help. =)
Gopher is fantastic at explaining how TES5Edit, MO and SKSE all work together.
Definitely worth watching his video's as MO is quite powerful in what it can achieve over NMM.
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