After Ewell was found dead, Atticus wanted to protect Boo Radley. I get that, but why did he want to have Jem, his son be the one who was responsible for the death?
I'll just stand over here being happy
Spoilers - don't read this if you haven't seen the movie.
Atticus didn't understand what really happened at first. The sheriff figured it out first, because he had seen Bob Ewell's body and the scene.
But Atticus didn't know at first that Boo had stepped in and saved the children. The only way he could see that Bob Ewell was defeated was that Jem must have done it. How Jem fought off a full grown man wasn't easy to understand, but maybe Ewell was drunk and Jem got lucky.
It was not until the sheriff challenged Atticus - you thin Jem killed Bob Ewell? Is that what you think, Mr Finch? - that Atticus finally understood the truth.