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The Nexus Mod Manager makes it easy.
It's just easier as well, as long as you know what you're doing.
As Craftian said, many mods can't be installed by Nexus manager, some because they are old and others, because they work differently to other mods (for example every mod or patch thinked to be installed from/to Main folder (Morrowind.exe folder) and not in Data folder (The code patch, the Morrowind graphics extender, etc or even the megacompilation that new users like to check first the MGSO, all them must to be unzipped in the main folder to start the installation after from there). Another mods need some little additional work (really little) as register the "bsa" files in the Morrowind.ini before start the game.
Most Morrowind mods, will be installed inside DATA folder (that's what Nexus manager do). Your data folder is in your Morrowind installation directory for example in steam versions usually: ...Steam\steamapps\common\Morrowind\Data Files, so exactly the same than Skyrim ones. Not only all your .esm and .esp files (what you must select/check after in your launcher or in Nexus mods manager left tab or in other mods manager programs, similary to skyrim mods) will be in in Data Files folder, but gradually, after installing mods the subfolders inside Data Folders will grow (textures, meshes, sounds, etc, etc). You need to know too:
1. Where to find and download Morrowind mods:
-"Morrowind Modding History"- Is the largest collection of mods with a big part of old mods and many new ones: http://mw.modhistory.com/
-"Nexus mods": have most new mods and some classic ones. Most mods here can be safely installed with the Nexus Mod Manager, but not all... Generally in every mod page you can find the "how to install" info.
-Great House Fliggerty: An old good page by one of the veteran MW modders. Old and new mods, forums and more. Some "exclusive" mods and hundreds of others: http://download.fliggerty.com/download
-Emma mods: Another old surviving page, some "exlusive" mods here, while others can be find in other sites too. Some great companion mod (Julan!) some good quests/new lands mods and the best children mod ever (far more complex and complete than Skyrim ones!):
There are many other sites, but most mods avalaible are in the aforementioned sites.
2. To install Morrowind mods manually:
As I said before, usually you only need to copy (or unzip) the mod data in Morrowind/Data Files directory, and check after the mod list (with the launcher or with some mod manager) to enable the selected mods.
Is good to read the readme files for additional install info, also.
Most patchs and some overhauls, however, must be unzipped in Morrowind main folder and later installed from there.
3. Nexus mod manager only can be used in mods that allow it in Nexus site, but is a good tool to simply download and store mods that you need to install manually (for example, download Tamriel Rebuilt or Morrowind Code Patch with the Nexus mod manager and later go to the manager mods storing directory (generally games/nexus mod manager/morrowind/mods but obviously depends of your chosen directory) to install manually later.
For fully nexus manager compatible mods, you simply choose any, push the download button, the mod manager that you previously install will open and download the file. In the right tab "Mods" you can see many categories that you can personalize with all your downloaded mods, simply click over one of them for install it, the left tab is a list with the most where you can enable or disable mods, reorder them, etc.
You said that your preferred mod haven't the nexus mod manger download option, but only manual isn't it? In that case you need to dowload the mod to whatever directory that you prefer and later unzip in the needed directory (depends what mod)
What mod do you like to install exactly?
you may check this guide
a guide for 2024 functional and very detailed.