As you compose this letter, it will be helpful to try to put yourself in her shoes for a moment, to get a feel for how she must be feeling. Imagine that your hard-working, honest, kind husband has been falsely accused of brutally raping and beating a woman that, in reality, he had just been trying to help. You know that your husband is innocent, but at the same time, you know that he will be convicted, because of the color of his skin. The father of your children, the man that you love, the provider of shelter, money and food, is going to go away forever for no good reason at all. And to make it worse, he'll be thought of as a vicious criminal. Basically, your life is ruined.
Then, think of how Atticus, a white man, stepped up to the case and pretty much proved to everyone there that Tom was innocent. It didn't change the verdict, but at least everyone would know, in their hearts, the truth of the matter. Atticus helped you to at least restore the reputation and honor of your husband. Atticus defended and did what was almost impossible: showed the racists for who they were, and your husband for the good man that he was. Imagine your gratitude. Imagine the comfort that you would take from that.
Now, take all of those feelings and thoughts that you felt while putting yourself into her shoes, and I would write it down in the most simple, basic terms possible. Since Helen can't read or write well, express yourself in words that are very simple, easy to understand, and uncomplicated. If you want to say more, pretend that someone is writing the letter for her as she says her thoughts out loud--mention that in the letter. So for example, "Dear Mr. Atticus: I am having Calpurnia write down my thoughts, because I can't write well, and I wanted to say thank you in the best way that I could." That way, you can have the letter not be limited by her weakness in writing. In the letter, express the sentiments above--your hopelessness at the case, your anger over your husband's reputation being ruined, your belief in his innocence, your gratitude for Atticus and the case he presented, your expressions that he is a good man and will be blessed, and that derived great comfort from the case and how it repaired your husband's reputation.
I hope that those thoughts can help to get you started; good luck!