BETA - Not really tested yet.
This is just a simple port of the Original Mod Multiple Custom Markers with Notes from Falouu! All credit is due to him.
https://www.nexusmods.com/skyrim/mods/38731


First Upload (0.2) didn't work! Fixed in version 0.2.1
Should have tested again after packing up. Had to use the loose files. SSE did not even start with the (original) bsa archive.


OK, should it be that easy?

Yesterday I was looking for such a functionality. I only found Jaxonz Map Markers (SSE Port). This only uses a static generic name for all world locations. Otherwise I only found two Oldrim mods: Multiple Custom Markers with Notes and Custom Map Marker Redone.

The author gave permission for Multiple Custom Markers with Notes. So I took a look. I only changed the master from "SkyUI.esp" to "SkyUI_SE.esp" with xEdit. And while I was at it, I opened it in the CK and saved it again - for Form Version 44 and whatever.
And it seems to be working !?

So far I've only set up a few (like in <10) markers and traveled a bit (like in the 2 hour game session last night). So far no problems that were not to be expected according to the mod description. Like that my beautiful colorful markers in the map are monochrome again ;-)

So I thought I'd upload it. Perhaps there are others who want to try it out. Then they might find a few things that don't work.
So if you have the time and inclination, please try it out and give feedback in the Posts.

But if there are problems I won't really be able to do anything. I have no clue about the development of mods, papyrus, SkyUI adjustments and what else might be necessary. I only started moding SSE a few weeks ago. However, the author linked the code in the original. In case anyone can do more with it. And maybe others have some ideas to help if you ask.



What follows is the Original Mod description from Falouu


NEW VERSION 0.2: Several bug fixes and improvements. See changelog below. 

IMPORTANT MESSAGE [august 2015]:

Hi,
I have got many requests to improve, fix and update this mod. Sadly I am
not capable of doing this. I don't even have Skyrim anymore!
So I have a little announcement:

If you are a modder, feel free to improve this mod and make it up to date!
You have my permission to modify and publish this mod at your own.

Sources of the mod consist of two parts :

• Mod files itself: https://github.com/falouu/Skyrim-MCMwN
• Necessery modification of SkyUi: https://github.com/falouu/skyui
  

Good luck improving this mod!

INTRODUCTION:
With this mod you can place your own markers on the map. You can give your
marker a name and write your own note to it. Up to 60 markers!
This is my first mod. I made it for myself, because I can't play without this feature :) And nobody created it so far.


FEATURES:

• You can place your own markers with your own, self-written notes attached to them.
• Up to 60 custom markers (if you want more, it's easy to add more in Creation Kit).
• You can fast travel to your markers.
• You can edit and remove your markers.
• Works with SkyUi's Location Finder.
• First line of your note become a marker name (displayed on the map and in Location Finder).
• English and Polish localizations.
• I only speak a little English. If you find language mistake, report it to me, I will fix it.
• This is very early release. It contains tons of bugs for sure. If you find one, report it to me.
• Limitations:
  ???- the spell works only in exteriors. Markers can only be placed on world map, not local map.???- As far as I know, there is no way to change default location name appearing on top-right corner in-game and in fast-travel messages. ????It will be always "Marked Location x". However, on the map it will show your own custom location name.

HOW TO USE:

• a spell 'Mark Location' will be added to your spell book when you enable this mod.
• when you cast 'Mark Location', your current location will be marked on the map.
• go to map, click on one of your markers and you will be able to edit note
  attached to this marker. First line of the note become marker name.

REQUIREMENTS:

• SkyUI 4.1
  

COMPATIBILITY:

• NOT compatible with all mods that modify "map.swf" file. For example all
  "Coloured markers" mods are almost certainly not compatible.
• It should be compatible with every other mod.
  

INSTALLATION:

• Nexus Mod Manager or manually.
• Manually: Only two files in archive: esp and bsa. Simply put them in Data folder.
• This mod needs to be loaded after SkyUI.
• If you upgrade from older version, see UPGRADING section
  

UPGRADING:

• v0.1 cannot be upgraded. Disable mod, save game, and install new version of mod.
  

BUGS:

• fixed or not yet reported :)
  

TODO:

• change custom markers icon on compass. Now is "AltairMarker" icon (probably
  unused in game), but ultimate icon is "PlayerSetMarker". "PlayerSetMarker" icon is currently displayed on the map, but not on the compass.

PERMISSIONS:
This mod is based on the SkyUI mod: http://www.skyrim.nexusmods.com/mods/3863
You will need to seek permission from me and authors of SkyUI mod before you can modify, publish or re-upload this mod.
Refer to the SkyUI permission instructions.


CHANGELOG:

• v0.2
  - BUGFIX: Fixed crashing on other than English or Polish game versions. (only "english version" file)???- BUGFIX: Fixed bug where marking location with previously deleted marker is not working after game load. ???- BUGFIX: No more marker corruption when casting spell in interiors (casting spell in interiors do nothing now)???- improved English translation
• v0.1
  - Initial release

video by Nozi87 (version v0.1):