Hello terminator,
thanks for bringing this up, for now the material "lakebed" means nothing and you can add/remove lake by choosing "sea" in the terrain and using it to place the lakes. Downside is, it is also for creating sea areas so if you locate too many lakes it will create a big unified water entity.
The current solution for adding lakes is not a good one. We will look into this to improve it, hopefully it will be solved in 1.07 already.
What might be interesting is that there will be a set of new lake textures in the next update, with four variations.
Here is a preview:
