Perhaps, you can create a custom model, like a flat plane, and add the texture of your logo on its surface, by having its height/width accordly to the resolution of your image. The black area could be, transparency
Hence, you can use the new model as an object and just place it anywhere you would like in the map? this way would be easier since you would not touch/edit the tiles on the terrain surface.
If you don't know how to use browedit I'm sure you don't know then how to create custom models, but if you want I can do it for you, since it would be easy. However, I need to ask you to post in Graphics Support, not this thread.
Oh wait. I'm reading a little more:
I was refering about just adding that logo on your map. Now, If you want to create animated gifs in ragnarok maps, thats not possible o_o ... Regarding the way how the water shows that movement, is, a very special case of how the clients calls it, and it goes specifically for water... not other element in the map.