I downloaded the Ark Royal file with tha ai but there is no flatten file so I created one but still the carrier sits on a mountain of water. Can someone help me? I have tried it on a clean FSX install so there are no other interfering add ons.

It sounds like you are missing an afcad or two. They are what you can use to stop the water issue. Check to make sure that all afcads from the package are installed.