Of course Atheist and Theist disagree at the most fundamental level, is there a god. That then leads to more questions about where things come from. The universe? Life on this planet? Man himself? There are some good arguments that can be made for each side but what they, Atheist and Deist, are doing is much more simple. They have made a decision and will find the facts that support that belief.
A good place to start is the creation of the world. According to the Bible the world is about 6,000 years old. That one is pretty easy to dismiss out right. If it is 6000 years old it was made to look a lot older. Point Atheist. Even the general formation of the solar system makes perfect sense and is hard to argue with. Where the Atheist will start to really lose the Deist is with the Big Bang. There must be something very mathematical about it because it is considered to be fact but even the die-hard Atheist must admit that the idea does sound a little flaky Besides, you are still left with the question of where did that subatomic sized piece of matter that has all the matter in the universe condensed into it come from? Did god make that? The one point that Atheist and Deist can agree on is that there is a forever. Alas!! There is some common ground.
Now that the world is here, by creation, science, or magic, where did life come from. Did we rise up from the muck or were we just created. The problem that the Atheist has here is spontaneous generation of life. For the right set of chemicals to come together in just the right way would be all but impossible, a Deist would argue. It would be like a tornado passing through a junk yard and creating a working car. That would be an unlikely set of events but is it a good analogy? Maybe not. Scientist have detected amino acids, a complex compound and the building blocks of protein, in the gases of Jupiter. Maybe given the right set of events it will always happen.
If that last part is true it poses some very interesting issues. The question is no longer is the life on other planets. It now becomes how much is there.