If you are converting from Nexus Mod Manager to Mod Organizer which I highly recommend the follow these steps:
Find your nexus mod manager file location. All the files should be .7z or .rar files. Nexusmods.com usually downloads in .7z
Copy your mod list with a screenshot tool from NexusmodManager. I personally use Snipping tool. But you can use anything.
Take all the zipped files and place them in a folder on the desktop. Name it downloads.
Disconnect the steam cloud sync. Click Steam from the steam interface. Click View > Settings > cloud
Make sure both boxes are unchecked.
Make sure to click okay to save the settings.
Verify the intergrity of your skyrim game. Skyrim > Properties > Verify integrity of game cache
When its done just close it out.
Place it in a new folder called Ordenador in your Skyrim main folder. Unpack to this folder. Place a shortcut on the desktop.
Run Ordenador. In the upper left corner select the file icon. Select the Skyrim data folder.
Make the boxes look like the following two images for Ordenador.
Then click. Select yes to resize images. And yes run a backup. This takes a while! When the black screen opens up leave it alone. Let it run.
IF at the end you get this error message:
Unhandled exception has occurred in your application. If you click continue the application will ignore this error and attempt to continue if you click quit the application will close immediately Argument number must be greater or equal to zero.
This is how you fix it. Create a new folder on the desktop. Copy the highrestexturepack 1 2 and 3. Paste them in the new folder. Reference the pictures above to run Ordenator. Check all 3 boxes for the texture packs then run it. It should be much faster this time.
Drop the texture packs back into the Skyrim > Data folder and overwrite.
Install all your mods. Either from your previous nexusmodmanager mod files (Some may be missing) Or install all new ones. To install from nmm. Click the Wrenches on the menu In Mod Organizer. See image.
Click the nexus tab. Enter your login credentials. Click associate with manager. Say yes to whatever it says. Click okay then exit out. This makes mod installation much easier to have to avoid manually installing everything. Everything you install this way shows up under the Downloads tab in MO. Double Click to install. If you have the file not set up properly do this.
Click the arrows until you see the data folder. Right click and set as data directory. When the green shows up in the bottom left corner you are good to go.
Make sure when you are done with all the mods your system is capable of having that you click the Sort Button Under the Plugins tab on the right side.
To run FNIS which is mandatory for all non vanilla animations you have to add a shortcut inside MO.
Extract FNIS to the Mod Organizer > Downloads.
When that is complete follow this default path to find it. Click the gears in the MO menu at the top.
Enter the title as FNIS
Select the Binary option first follow Mod Organizer > Downloads >FNIS Behavior 6.3 > Data > Tools > GenerateFNISforUsers > Click on the GenerateFNISforusers.exe
Next leave Start in Blank! When done close it out by clicking okay. Select FNIS from the dropdown menu and click run. This will launch it.
Also when you click SKSE to run Skyrim you have to run as admin. Make sure your properties on SKSE.exe in your skyrim main folder looks like this!
Credit to this Youtuber, the Anonymous Patriot for helping me create this tutorial!