I think the best way to difference them would be to reskin the hull. In the picture that Wolf have posted, the hull si much darker. Maybe an only CnP of a good wooden texture will do the job and it will look less like the carrack.
Also, if you lack of some model, look here :http://forums.civfanatics.com/showthread.php?t=209775&highlight=shipyard there are some medieval ship that could be use for different carrack. There is also a lot of good ancient ship (I know your still in the age of discovery, but if you want to make ancient ship... it will be usefull).
Also, if you lack of some model, look here :http://forums.civfanatics.com/showthread.php?t=209775&highlight=shipyard there are some medieval ship that could be use for different carrack. There is also a lot of good ancient ship (I know your still in the age of discovery, but if you want to make ancient ship... it will be usefull).