Sorry. I wish I could help you there, but ...
When I want to put something under water in FM8, I:I've been struggling with creating just-under-the-water-features like reefs, sunken islands chains and the like. All the images I've found on Google show them clearly - I'm just not finding a technique to recreate them properly. Some seem to be only a couple feet under water, and close enough to the surface that a person could walk across them if they wanted.
1) Put the water onto the map first.
2) Put the object that's supposed to be under water on top of the water.
3) With the intended underwater object marked, I move the transparency slider to the left until I have exactly the underwater effect I'm seeking.
I'm not sure if that will solve your problem, but up until now, it's always given us exactly what we've been seeking.