To make the levels in Unity, I started by assisting the full-time level designer that worked on the project with making designs for the levels using Adobe Photoshop and Paint.net.
Next, I built the levels out in Unity using the Tilemap system. Then I would thoroughly test the level to make sure it had no issues with collision, and to ensure it would be a fun level.
I also had to create maps of the world to ensure proper pathing throughout them, and to tweak the pathing to make it easier for players to understand.
Finally, I used text fields in Unity to add monster formations to every enemy in the game, usually giving two or more possible encounters per enemy.