1. I suggest add new static water tiles to empty slots at art mul. With mulpatcher or uofiddler
2. You need to use centred or centred+ map editor for elevation of land tiles or etc.
Firstly you dont need to change landtiles(textures).
Secondly you need depth to see efect of transparency.Example landtiles(best is sandtiles) z -20 and transparent static water tiles z 0.
And be sure static water tiles have transparency marker at tiledata
i used google search for clouds pictures.then find some and in photoshop or something likethat (i used photofilter 10) edit them. after add statics clouds. finally add them in to statics muls. give them transulent and transparant ( from tiledata settings). can better view if you edit patiently...