Preparation
Before installing the mods, a couple of
other files has to be installed


1 - If you haven't already, sign up at the Nexus.
(LINK)
It's free, and it takes 2 minutes. The Nexus is a great site for mods in general, so it's definitely worth your time.

2 - Download and install the NexusModManager, "NMM". (LINK) *Install descriptions are found at the Nexus page if needed.

3 - Download and install the Skyrim Script Extender, "SKSE64". (LINK)
Download the latest SE version. Unpack the file and move the content of the SKSE folder into the Skyrim SE game-folder.
Inside the Skyrim SE game-folder, rename "SkyrimSELauncher.exe" to "SkyrimSELauncher.exe.backup".
Then rename "skse64_loader.exe" to "SkyrimSELauncher.exe".

4 - Download and install SSEEdit. (LINK)
Unpack and copy the files to any folder, then make a shortcut to "SSEEdit.exe".
This tool is used to clean up Bethesda's "lazy edits" from their DLCs. See description in the Cleaning section. (LINK)

5 - Download "TES 5 ESS Files Editor". (LINK)  *It's made for the "old" Skyrim, but works perfectly for SSE as well.
Download the latest version and unpack the files into any folder. Make a shortcut to "TESVESSE.exe".
*If you plan to start a new game after following this guide, this file is not really necessary, but I still recommend downloading it just in case. If you want to continue a saved game, then you definitely need this tool. It's used to remove old script data from a save-game file. Unfortunately Skyrim stores scripts in the save-game files, so if you remove a mod which contains scripts, then the scripts stay in the save-game, and can cause all kinds of errors.

6 - Download "xSHADOWMANx's Dll Loader". (LINK)
Download the latest version and unpack into the Skyrim SE game-folder.

7 - Download "SSE Engine Fixes". (LINK)
Download both files manually, and unpack them into the Skyrim SE game-folder.

8 - Launch the game to see if everything works.
Most importantly, check if SKSE64 is loading correctly. A lot of mods rely on SKSE64, so this is very important. - All it takes to fail is one misplaced file.
To check this, bring up the console* in-game, and type "GetSKSEVersion" without quotes, and hit Enter. If the console shows you a version number, then everything works. If you get an error message, then you need to look at the SKSE files again and find out what went wrong.
*To bring up the console, press the upper left most key below the "esc" key. "~" on US keyboards, "" on EU keyboards.
Steam users: If you replaced the files as recommended in point 3, you should be able to launch the game via Steam as usual.

9 - Make some coffee and get ready for several hours of downloading and installing. It's a long time, but remember at the end you will get the result of several months work.

 

When done installing these basic tool, please proceed to the cleaning section before going to the mod-list.
Proceed to Cleaning

 

 

Curious if the results are worth the effort? Here are a few before/after screenshots to give you an idea

Before/After Screenshots

BEFORE                                           AFTER                                                    BEFORE                                            AFTER