So let me get this straight. You want to edit a layer at runtime with script, this is possible. You can't move a layer left or right, or even up and down. all layers are aligned to the top left corner of the map and scroll from there. (The top left pixel of every layer are always stacked on each other perfectly) If you make the scroll rate zero then the layer covers the whole screen and doesn't scroll ever. (remember use Map and not MapEdit since MapEdit is only for when you open the map editor in the SGDK design environment.)
As far as doing a day and night sequence, I don't think it is possible, since there is no alpha transparency supported. The only way I could see doing something remotly like making a darker tint would be to make a tiles set with 2 tiles each 640x480 one transparent, one darker (or dithered darker/transparent), and then make a tile animation that switches between them once/frame. Then, make the top layer of your map scroll rate=0 and use this tileset. Then with script, change the value of that tile depending on if it is day or night.
It would probably look pretty bad, but could work (would probably look a lot better if you made the tileset 3 tiles, and had two of them dithered opposite and cycled between them at night)