Trying to rotate part of an Fbx Model

I am making my first game in Unity 3D something like tower defense game. I have imported a Fbx model of a tower and attached it to a prefab. Now I want the nozzle of the tower to rotate and follow the enemy as the enemy passes by . In the fbx model i imported i got I have two poly meshes one for the base of the tower that is fixed, and one for the top of the tower that will rotate. Now I tried to create two different gameObject with these two meshes but if I put them on same point they overlap. So I have to do manual alignment such that the nozzle sit correctly over the base. I was wondering if there is any other way such that entire towers remain is one gameObject and I can rotate the upper part.

Have the upper part of your model as a child over the main part, then add the script that controls rotation only to the child object.