How did the universe fit into the size of an atom?
The initial singularity that is theorized to exist prior to the beginning of the Universe would have been infinitely dense. We can't really understand how this would have been since it is not an observable phenomena. The most similar thing would be the singularity of a black hole which is said to have infinite density too, but some infinities are bigger than others.
For example, there are an infinite number of numbers between 1 and 2, you just keep adding decimal points. Now there are an infinite number of numbers between 1 and 3 as well. The second infinity would be large than the first infinity. Using this logic the singularity of a black hole would be like the number of numbers between 1 and 2 and the singularity of the big bang would be like the number of numbers between 1 and infinity.