Step 1:
Don't try to fit yourself into a predetermined level structure. Instead, build the level structure around what you want to design. Saying there's a super-duper underground airship boss level is kinda meaningless if it never makes it past the planning stage. Figure out what you think would be fun to design, and do that.
Step 2:
Suddenly your episode seems pretty empty... oh well. You know the basic story, and the way from beginning to end is for you to shape and reshape. Over time, more levels will join the small selection currently part of it. Whenever you get ideas, see where they might fit with what you have in mind. It's a lot less stressful than having 20-30 more levels to do in the backlog, which can be rather draining!
Step 3:
In order to get ideas, you need to know what you can do. Familiarise yourself with the contents of the editor. Layers and events are nice and all, but if you don't know fun ways in which you can use a Goomba, they won't get you far. A lot of tools are viable for great levels, and if you explore them you'll surely find something fun you wanna turn into a level. A couple of my favourites are: P-Switch, Bubble, Conveyor Belts, Bombs.
Step 4:
It's important to think about what purpose elements in your level have. The easy way out is to make a horizontal stretch of land and fill it with enemies. Might be a tranquil experience in the end, but might also be boring. What I recommend is thinking of elements (Blocks, NPCs, autoscroll, etc...) in terms of their properties and what they'll do for you. For example: A Goomba is vulnerable from the top, but it's dangerous if you're below it, and it can fall off ledges. Familiarise yourself with such properties to find different ways in which to challenge players.
Step 5:
Testing goes super fast if you focus on the important elements of the layout first. A crude floor might not look nice for now, but when you have to adjust ledge lengths to get the Goomba to fall juuuust right, you'll appreciate not having to dig through tilesets until you're satisfied with the result. An obstacle in which elements work together to get the player to overcome it is called a "setup". Here's an example using Goombas (G) and the Player (P):
Step 6:
That setup above alone won't win any oscars for incredible performance, but that's fine. Levels aren't just one setup after all. At this point it's helpful if you have a theme for your level. No, not visuals. I mean in terms of gameplay. The theme may be influenced by the visuals, but it determines the kind of obstacles you'll encounter. Let me explain:
Take the screenshot above for an example. The action the player performs is jumping past enemies from below. There are countless ways to mix this up later on in the level, creating unique obstacles by just swapping out the NPC inside the little staircase. Spinies provide the same obstacle as Goombas, except you can't kill them from above either. Bullies bring in a new dynamic by following you around, etc...
Another example: A level in which you face a lot of spinjump challenges suddenly throws a new setup at the player: A bridge of turn blocks on which a variety of spiky enemies from earlier in the level are gathered. The bridge stretches for several screens and has gaps and different levels of elevation. The player has proven so far that they know how to use the spinjump to get past obstacles, but can they do it without?
Step 7:
Ask your friends for input. Coming up with a couple dozen setups for a level can be difficult, especially in the beginning. I recommend lots of experimentation in the editor, of course, but ideas from other people are powerful as well. Maybe they'll instantly come up with something cool you never even thought of!