Here is how we edit levels in Godot Engine, first we make a mockup of the level, digitize it with correct proportions and put it as a guide inside the editor, then we place each asset following the image as reference.
This image is the first version of the alpha level, a temporal level with the purpose of testing the feasibility of some mechanics from later levels and stress test the engine.
On the top left of the image are the enemy paths featured in the last videos from this post and this one. Also You can see how the level looks ingame on our last video post.