I've managed to make a first floor of a castle perfectly, but I cant figure out how to get tiles on the 2nd floor. As of now CentrEd wants to raise the first floor tiles to the height of the 2nd floor and that virtual layer thing, I have no idea how to use. So how can i create multiple floors?
I'd say that you are trying to create the second floor with terrain not statics which raises the first floor...
Uncheck the "Terrain" checkbox above the tile list, find the floor you want, set the virtual layer on the desired second floor height and place the static items on the layer.
Or you can force the height of placing static tiles in the "draw" menu.