I think you should focus on the ultimate result.  What do you need the interaction between the sub and the water to look like?  What do you need a primative to do to generate that interaction?

By producing this as a series of stills, you can combine  isolated key frames and see what is happening. 

Theory only, but is there an after effect program component that can produce the bow breaking foam and spray and side and stern wake as a 3rd layer?