I dont know where to begin but I am pritty upset about all the stuff being written or not being written about MOD LOAD ORDER.
First of all, why isnt there a sticky with an easy three step guide on how to properly load your mods?
Secondly, there seems to be all kind of information about what to do or what not to do and its really confusing! It took me a few weeks to realise im doing the wrong thing, and Im not completely sure I am at this very moment!!
Thirdly, there is a thread with a long explanation of things ( http://www.gameskyrim.com/topic/1353517-important-load-order-and-you/page__fromsearch__1 ) that is so utterly complicated and confusing that it only adds up to the pile of cr*p that can be read on the issue.

I am now using BOSS to sort my mods ... or so I believed... until I read somewhere that BOSS doesnt change the load order for you AT ALL (although it is explicitly written that it does on the skyrim nexus site)... It merely tells you what the load order should be.
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So I load up my favourite mod ordering software, Nexus mod manager, since someone told me : "use your favourite mod load order software, such as NMM, to order your mods". Of course, NMM doesnt do that EITHER! .... So currently I believe that I need to use skyrims own software ( SkyrimLauncher) to rearrange my stuff manually. This however, changed my heavlily modified .cfg file that governs my graphics settings so All those hours spent on trying to optimize skyrims graphics are lost. Then, even after using Skyrimlauncher - NMM doesnt recognize this and keeps telling me my load order is something else.

To worsen things even more, I cannot use skyrimlauncher to launch the game since I need to use something called Skyrimscript extender which is run through NMM...

Could someone, who really really REALLY knows how to do tell me once and for all? And please... if you feel that you might not know 100% for sure - DON'T!

And then a moderator could put up the instructions as a sticky - It would have saved me hours instead of reading 10 threads á 10 pages that has given me nothing except confusion.

cheers!

This is overly simplified but that's what you asked for

1. Load order was broken by the steam workshop
2. Bethesda fixed load order by radically altering the way it works, this broke all the mod organizers and load order tools
3. Bethesda did not document this change effectively so it created great confusion and delayed fixes to all the broken tools.
4. The only reliable method of changing your load order currently is to Open your plugins.txt in a text editor. plugins.txt is found in your local application data folder. On Windows Vista/7, this is C:\Users\[username]\AppData\Local\Skyrim\plugins.txt.
5. For more detailed information go here http://www.gameskyrim.com/topic/1356991-important-load-order-and-you-2/

If this is too much trouble, NMM will reorder and read plugins.tst, also. But no auto-sorting, yet.

So whats the boss plugin now incorporated in nmm for?

It is in the process of being implemented. Right now, until BOSS proper comes out of beta, NMM won't be able to auto-sort. Remember NMM is still in beta, too. An open beta, but still beta.

I'm guessing because, like Wrye Bash, NMM will have boss built into it.

When BOSS is updated to write to plugins.txt automatically, it'll be seamless.

You are in luck my friend, I recently found myself in the same boat. Here is what I learned, it might not be 100% correct, but it seems to jive now with what I'm seeing.

Ever since a patch or 2 ago, the mod order is determined differently then how it used to be done (and in past games).

There is the file mentioned about, plugins.txt. Located where mentioned above. In that file is the load order that Skyrim will use. Specifically it loads the mods in the order they are listed (first at the top, last at the bottom). The way Skyrim works is the LAST mods loaded (ie near the bottom) take priority. Ie. if you have two mods that change the same thing, the last one loaded's change will be the one that the game sees. This is why load order can be an issue in the first place. If you have two mods and you want to make sure one doesn't influence the other, generally you make sure the more important one loads after (so it's changes are felt).

The newest versions of Nexus Mod Manager will allow you to edit this file using the standard NMM load order interface. (Hitting the arrows to move items up and down). The top of NMM is the top of plugins.txt, the bottom of NMM is the bottom of plugins.txt

What you might be seeing: this didn't work for me, no matter how I changed NMM, my plugins.txt wasn't changing. Turns out on some systems you have to go to the folder that the file is in, view it's properiteis (right click yellow folder, select properties) and unheck the "read only" box. When that is set windows will not allow you to change the file for some reason.

If you do that, you can go back to using NMM and it will actually affect the load order of your game. Why this is nice, is that NMM allows you to turn mods on/off without losing there order. (You'd have to do it manually with plugins.txt).

What none of the above will do: is set the load order for you. You have to decide what the best order is, you have to move them to that order. I don't use BOSS so I can't comment on what effect that has, only to say that while NMM downloads it, it doesn't actually use it yet. So it's all you.

Again, generally the more important the mod, the later you want it to load (and lower down the list). NMM will list files with "master" dependencies (you can see that info on the right). Generally a mod must load AFTER any master file dependencies it has.

So again, check the permissions on the directory, to see if your plugins.txt file is being prevented from changin. Once that's fixed, you can go back to using NMM to change your mod order, and that should work. Definitely stay away from the launcher, as whenever I touch it it always messes things up.

This might help:

http://www.gameskyrim.com/topic/1357914-just-a-thought-about-pluginstxt/page__p__20475351#entry20475351

Here, I propose a temporary approach for converting old school load order information (file timestamps) into new style load order information (plugins.txt).

And, within an hour of posting that, deaths_soul posted another approach in that thread, with a download link. (But I never got to play skyrim last night, so I did not test either approach... sorry about that.)

What's the load order for?

Another problem discovered... windows 7 doesnt by default allow me to see that I have a folder called AppData... DOH!!!!!!!!!!!!!!!!!!!!! Had to enter it manually to get there... *sigh*

I cannot understand why software - like NMM or BOSS - that is relatively advanced cannot write the load order to a text-file... its the most basic thing that exist...

Because they're programmed by people. Version 15+ of NMM can write to plugins.txt, and there is currently a closed beta of a version of BOSS to work with threw new patch. Right now the only thing to do is be patient, things are being worked on.

It is not only about writing a file. The plugins.txt does include only active plugins, so the inactive ones must be remembered - including their order. Furthermore, till the patch the load order has been determined by timestamps on the files, which is now completely irrelevant - yet, you have loadordering (including BOSS) based on this, so you have to develop the continuity for older load orders transforming into the new one seamlessly.

And to be blunt - you don't know, why it is taking so long, because you don't develop the utility. So you don't understand. Beta testing, bugs....

If you updated NMM after the change was made to Skyrim, then it can and infact does write to plugins.txt. However if your Windows Filesystem's permissions are set up to prevent that, then it can't. Unfortunately NMM doesn't ever let you know that there is an error when trying to write to plugins.txt. I had to go and fix the permissions by setting not the file itself, but the folder it sits in, turning off the "read only" checkbox.