Use this phrase when you're describing things in order, especially for instructions:
First you fry up the meatballs and set them aside. Then you chop up some onions and celery and cook them on low heat for about 15 minutes. After that, you add the tomatoes and garlic.
You don't usually use "after that" for the second step in the list, but you can use it for the third or any other step after that.