Rearranging plugins/ stopping doubles

I have a problem with two plugins.

One is the Morrowind Add-on Pack.esp and the other is the Seyda Neen expansion.esp. The problem is that the buildings and ships are stacked on top of eachother. Seyda Neen is much bigger and much more fun but it also looks like a mess.

I have been trying to move things around with the construction set and inside the construction set it looks fine but in-game it looks their are duplicates of all the stuff I changed. For example when I moved a ship a dopplegager is their in its original position.

How do I change the plugin so there is only one of each npc and object?

Thankyou