Preparation
Before installing the mods, a few
other things have to be setup


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 the official DLC-files. 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.
To check this, bring up the console* in-game, and type "getskseversion" without quotes, and hit Enter. If the console shows a number, then everything works. If it shows 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 a US keyboard, "" 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 will take some time, but in the end you will get a result that otherwise would take several months to obtain.

 

When done installing these basic tools, 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