The issues are not with WED ^_^
1) I attached a level to my main script in "Map properties" window.
You mean: You attached a script to a level.
There are TWO KINDS OF INCLUDES:
#include <mtlFX.c> //Default files
#include "thisoniscustom.c" //custom files
2) I opened the 'bed01' prefab in WED
Dont. Make a model insteand. your killing your resources for an ugly prefab.
3. No. Dont. Model instead.