These are the mods I use when making maps.

My technique. Explained.

It's important to unsubscribe everything not needed and only subscribe to items you are willing to include as a requirement. Anything plopped down but not included as required item will popup in players' loading screen in red. I even turn off DLC's that are not needed. Only subscribe to required items for the current project and make a Collection of required items for the map as you decide. That will serve for publishing the map as well. See this as 2 steps in one, not as an extra step!

Map Editor's new Map created
I use the Map Editor at the beginning to import heightmap or craft the basic shape, depending on the project.
You will need to go through the game's MapEdtr hard coded requirements, but it's important that the outside connections you place here remain until the ultimate release. This is important or you may end up breaking the savegame (if at some point in time you delete one of those...)

Chosing the biome is a one chance deal and it's now the time to decide. You can change the Theme as many times as you want, but you will need Environment Changer mod (and your subscribers) if
A. You chose a different biome than the wanted Theme's default
B. You want to change biome period. So your choice here matters. Vanilla maps can't do this. The theme - biome combo cannot be changed.

Once the basics have been covered, Start a new game
The fun begins when you realize that all you can create can always be brought back to day 1 and only have to worry about the map. Every vehicle or train you see just wants to get through the map!

Working from in game
Working from in game makes every aspect of map making a lot more enjoyable. Higher definition terrain, no surprises on network junctions and terrain collision.

When the work is done, it's time to go back to the Map Editor and finnish the work. The following tasks are kept for that step: Trains, Planes and Ships paths are done from the Map Editor since, even though made possible by More Network Stuff mod, these can be buggy at times and you want to take no chance when it comes to map making...
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First you will need to subscribe and activate ModTools.
https://steamcommunity.com/sharedfiles/filedetails/?id=450877484

Then you will have to prepare your savegame as everything (buildings, props, etc) will be imported into the map editor. I'd suggest you use the MoveIt mod to delete every single item but the trees.

Go back to the main menu and open up the ModTools console (F7) and run the following script:

Originally posted by boformer (original script by samsamTS, later fixed by Ronyx69):

ColossalFramework.Packaging.Package.Asset latestSaveGame = SaveHelper.GetLatestSaveGame();
SaveGameMetaData saveGameMetaData = latestSaveGame.Instantiate<SaveGameMetaData>();

LoadingManager.instance.LoadLevel(saveGameMetaData.assetRef, "MapEditor", "InMapEditor", new SimulationMetaData() { m_WorkshopPublishedFileId = ColossalFramework.PlatformServices.PublishedFileId.invalid, m_updateMode = SimulationManager.UpdateMode.LoadMap}, false);

This will automatically load whatever the latest modified savegame there is into the map editor.
Source: Cedar Valley Official Map, by Strictoaster
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As soon as I'm in the Map Editor (launched from the script), I save the map and quit. I then unsubscribe Modtools and restart the game. It's now time to load the Map Editor (with the newly created file) and prepare for publishing as you normally would.

The only down side of this technique is that players using 81 tile mod will need to save their new game, and reload it. On the first load (new game), terrain will not be full resolution and roads within the center 25 tiles will be missing the surface texture.