Hi!
You can't and don't have to align floor/ceiling textures (=flats). They align automatically into the grid in which you place your map.
If you want to make a teleporter, just draw a 64x64 square exactly above the lines of the grid.
The ceiling texture is F_SKY1 and it uses the texture SKY1, 2 or 3 according to the map number.
The sky is a ceiling texture, so you find it in the list of flats.