Hi, Lydia. Welcome to CatholicInfo.
I actually experienced the same thing nearly a year ago. I never became an atheist, but I kept having bad, atheistic thoughts. Thoughts like "how is it possible that there is a God?" and so forth. The thoughts were really annoying and scared me a bit. Fortunetly, they went away after much prayer. And now whenever they enter my mind, they don't phase me because now I know how to refute atheism and evolution.
See, those thoughts you are experiencing are from the devil. The devil likes to plant thoughts like that in the heads of people he knows are vulnerable to get them to doubt that God exists. In fact, one of the devil's greatest ploys is to get you to think that he himself does not exist, because if a person doesn't believe in the devil or hell, that person go about his life committing sin after sin at a care-free rate, and his soul will be in hell after he dies. So that is one trick the devil loves to use. The key is to be strong enough in your Faith to fight them.
The way I fought my thoughts was by learning how to refute atheism and evolution. I recently studied Christian biology, something that helped me tremendously. I can't go over the whole thing but to give a brief summary: Charles Darwin is credited as the "founder of evolution". Early in his life, he was a Christian who "believed in every word of the Bible". One day he took a role of observation on the HMS Beagle, and began reading the work of several atheists that influenced his own beliefs, i.e that animals "compete for survival" and that "the present in the key to the past". After reading this, he began observing numerous different creatures, and eventually concluded that evolution was responsible for creation. Now, interestingly he never became an atheist. He apparently was a Deist, someone who believes there is a God who created the world, gave it it's first push to get it going, then left it to work on its own. Deists also believes that God allowed evolution to take place.
The problems with the evolutionist theory? To name a few, there are no "intermediate links" that have been found in the fossil record that scientists need to "prove" evolution occured, and also the evolutionist theory claims that animals "compete for survival". In reality, however, many animals work together in order to survive, a fact that defeats evolution. But the biggest thing is that there is no way that the complexity of creation could have occured without a Devine Creator.
Basically you have either two options: you could either say that there was nothing and that out of nothing there became something, or that God was responsible for all creation. Atheists say the latter makes no sense, but how much sense does the former make? Something can not suddenly be made out of nothing on its own, that is absurd.
I hope my post helps. I suggest you continue to research the flaws of atheism and the evolutionist theory, and I suggest you seek guidance from a Traditional priest. I'll be sure to keep you in my prayers.
God Bless.