How I believe the water should be build:
1. Making a rough cutout of the island
2. Refining the rough cutout
3. Remake the parts of the refined cutout where the tunnels will go, thus making it possible to assign a different water type to these ocean tunnel pieces
4. Make the layers according to what you've build in 3
5. adding of pools, pools, etc...
I'm not sure about 5 being the last step. It might be the game reads the water.dat in a certain coordination order. I'm not sure about that though.
I need control over all the water where the tunnels run underneath.
Then I guess you'll be in control of all the water (give or take point 5). You can't make 4 without 3, 3 without 2 and 2 without 1. So a new problem comes foreward. Either you learn how to use the Max script, do it al by hand (that's a fun one, I tried that once), or wait for ReSpawn to release his G-tools water editor.