Start off with a nice room. Base it off a room at work, at your house, or another indoor place.

Notice how, as the stairs go up a level, the wall is only 2 tiles up, rather than the 3 tiles up in the rest of the room. That is one way of adding the stair effect. there is also making it one tile up from the previous room to add alittle more of a natural flow.
Alright, now its time to add the items. Here are afew tips to making the room like this:

-Make sure to add things at the bottom of the room, right under the roofing. Things can be on every wall.
-Events arent only for NPCs. It can act as a third layer so that you can add alittle bit of depth.
-Rooms dont have to be humongous so you can fit as much as possible. Make it smaller for more of a realistic effect. The hero doesnt need too much space inside a room.
-Make sense. To the top right is a storage room. I have boxes, some cans, and a small bin. In the engine room, I have two cans, one connecting to the machine itself, a control panel next to the machine, and an extra can(theres no room in the storage room)
One thing I forgot to make was a door. Just make it go 1-2 floor tiles down at the bottom, or a door event at the top. Heres an example of the floor tile at the bottom.

Yes, the barrels are over the shelves. Try to avoid that while making a game.