I have not read all the books, and those I read, I did so long ago. I just can’t find out whether Ender ever knew he killed Stilson and/or Bonzo. On the one hand, it would play along with his guilt feelings. On the other, it would be symbolically sound that he did not know about these “steps” toward xenocide.
Yes. He saw videos of the fights and the aftermath.
And there was the matter of the court martial on the crimes of Colonel Graff. Admiral Chamrajnagar tried to keep Ender from watching it, but failed -- Ender had been awarded the rank of admiral, too, and this was one of the few times he asserted the privileges the rank implied. So he watched the videos of the fights with Stilson and Bonzo, watched as the photographs of the corpses were displayed, listened as the psychologists and lawyers argued whether murder had been committed or the killing was in self-defense. Ender had his own opinion, but no one asked him, Throughout the trial, it was really Ender himself under attack. The prosecution was too clever to charge him directly, but there were attempts to make him look sick, perverted, criminally insane.
Ender's Game - Chapter 15: Speaker for the Dead