Hi AJ
I'm afraid you have hit the 'hump'. I am going to assume that you have put parking spots on both carriers with afcad because the end result of that is the hump you describe.
In order to prevent this happening you need a specific type of afcad file, that is a second afcad for each carrier with a separate ICAO code. That consists of an apron, at sea level, which is at least as long as the aircraft carrier though better somewhat longer, I usually go for around 1000 - 1800ft, and around 800ft wide, I have found one place where a width of greater than 800ft was required but it is normally sufficient. That apron can be of concrete, it won't show, but again better to be of a non material (that is not an option within the afcad program it has to be done another way).
The 'trick' with this one is where it is placed. You will need to make a new folder. In FS9/Addon Scenery make a folder called 'Top Level' and inside that make another folder called 'scenery'. Copy the sea level afcad into that scenery folder. When next you start FS you will need to activate that folder in the scenery library, it is a requirement that this scenery is at the top level, above any other scenery that the contents may apply to. When first activated it is at the top of the list, as you may eventually have other files in here, as I have, you will find it easier if every time you install more scenery you simply move this one back to the top. That deals with the hump.