I am going to answer all your question per my memory and I think all of answers are in the movie itself -
The alien has created a device from the various stolen electronics attached to the base of the tower which makes metal devices attracted towards the water tower. Alien doesn't want to attract metal but wants to collect all his cubes.
Military didn't leave the cubes around in the town but they are trying to research on the cubes' technology and the train crash is the reason for the cubes to be distributed in town but still most of the cubes are still with the Military.
Alien is trying to create a device which act as a magnet to attract his cubes from all around the town.
I didn't get the 4th question, so I am not able to answer it.
The cubes are all responsible in making his ship, it's like if the alien has all of the pieces of cube he can easily make a ship.