Note that this Editor does not work like the GTK Radiant, Hammer Editor or similar ones.
Setting up Notepad++:
Follow this
Link.
Overlapping floors & thin ceilings:
As you use texturized plane-primitives for this they acutally will be "thin" and mainly just visible from one side.
If the floor's overlapping try to scale it down or use more primitives for one room if it's not just "a cube".
My advise concerning the stair-thing:
Use another stair entity to use as a ceiling. Be creative.
Parts of the wall missing:
Like primitives, solids are mainly only visible from one side. So if you place your wall facing the wrong direction, you will see through it.
Glitching Lamp:
Just turn off grid snapping and arrange it yourself. Not all entities fit with solids.
There's really no typical size for a map. Mainly it's like from 500KB to 10MB.
And yes, you would put your custom entities in you custom story's folder.
Greetings
Dr4konite