When I model any sort of terrain, I typically end up with only one uv map over the entire terrain in order to avoid clutter. Having to deal with multiple diffuse and normal maps can make things tedious when you need to make simple texture changes.
As far as water is concerned, it should never be a part of the terrain mesh itself (as you probably already know). I say this because water should be permeable (a player can pass through it). Modifying a single mesh's triangles to allow permeability on specific parts would take more effort than it's worth.
Oh and by the way, water UV's in EQ zones are very simple. They use a tiled planar uv map. That's it. The scale is something like 2:1 or 1:2 (AFAIK). But it sounds like you've figured it out.
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