Hello everyone! I missed a lot of posts.
I was using a system much like the one adriweb was proposing. I have classes with all the necessary data and methods for each object type. Then when I create a new instance of the class, I store it to a table. When each missile moves, I check to see if it is touching any enemy object. If it is, a method is called which in this case, deletes both the enemy and the missile. In the future, it will probably trigger an explosion animation too.
The scrolling will be skippable. I just wanted to emphasize that this was a demo and not the final product yet.
I hope every one had a happy holiday season this year!