I will try to answer the beginning of your question: "Answering Atheist". For the second part "about Torah miracles" there are already dozens of good answers. I will only try my 2 cents.
In this answer I will assume you care very much about the person you are talking to and you both care genuinely about finding the truth. If this is so you two can try to find the truth together, search books, argue, and so on... From this type of discussion you can gain very much. If this is not so, maybe it is pointless to argue, as Monica said.
I think, first of all, you should seek your answer to those questions. What do you think constitutes a miracle? Do you believe those miracles are true? And why? If you feel you are unsure about your own positions think deeply about them. You should not think in defensive ways, you should strive for the truth. If he is right, he is right, but before you act consequently (maybe the Torah is not right, after all), you should be sure that he is right.
A good idea is to go to a Rav that can handle this type of questions (Torah vs Science) and to bring your friend with you. Then ask the Rav what is the answer to the atheist's claims. If he cares about the truth, he can gain from speaking with the Rav, and you, too, can learn very much.
A Rav is only one of the resources you can find and it has not to be a Rav, it can be someone with enough familiarity with the topic. You can search proofs on your own (many are provided as answers to this question) that help you to defend and strengthen your position.
I feel somewhat obliged to share my position about the topic. I believe in spirituality and I feel a connection with Hashem. I know that he answers my prayers, for example. So spirituality can influence reality. I cannot explain how, but I know for sure that if Hashem wants something, he obtains the result. From a religious perspective it doesn't matter very much how. I happen to have a degree in Physics, and from what I learned, I know that there are "principles" or "fundamental theories" that are universally believed to be true because no experiment ever contradicted them in a fundamental way (e.g. conservation of mass/energy, uncertainty principle, the fact that a "theory of everything" should have a flavor of QFT and involve many fundamental symmetries thus implicating conservation of many quantities by Noether's theorem but I am really digressing now...). My position is that: (1) it can well be that a miracle produces something that contradicts these natural laws (2) there are many ways that almost all of these natural laws can remain true. I can myself come with some (what if we take quantum perturbations of slim probability into account? or, more simply, some geological or biological curiosity? there are so many thing that are possible but don't usually happen!). You can also find that the Torah itself, when interpreted through a Midrash or just a small insightful consideration, can change its face (maybe the "taninim" in the Genesis are dinosaurs, or Adam had relationships with hominids...). It doesn't make much sense to stick with one "natural theory" and one interpretation of the Torah and make them collide!