We learn early on that Bob Ewell is not a very nice man. He is vindictive and wants to make those pay for things that have happened to him. He blames Atticus for all of his problems, and he knows the only way to make Atticus pay is to go after Jem and Scout.
Now that Tom is dead, Bob knows that the only two left to deal with are Jem and Scout. He knows that by hurting and even killing them, this is the only way to really make Atticus pay. Bob feels like Atticus is the one for all of his problems. He sees that the only way to get Atticus out of the way is to take away what matters most to him, which is his children. He attacks Jem and Scout after the Halloween pageant and nearly kills them. Boo saves Jem and Scout that night and Atticus thanks Boo for his children. Atticus knows exactly what kind of man Bob is.
When Bob says "One down... two to go" he is talking about getting rid of Jem and Scout. He has already taken care of Tom and feels that getting rid of Jem and Scout will teach Atticus his final lesson.
Readers learn quickly exactly what he means. He intends to go after the Finch children. Ewell is vindicative. He feels that he was embarrassed in the courtroom and his pride has been hurt. Tom was the original cause of this shame, but Atticus carries just as much guilt. It was Atticus' cross-examination of Ewell and Mayella that showed the town what life in that household was really like and who was at fault for Mayella's injuries. He means to go after the children as the best way to hurt Atticus. To kill him would not be enough. To kill the children would cause him more pain and suffering.
Ewell’s statement is meant to be a threat against Scout and Jem. While it is true that Ewell is mean-spirited and vindictive, he also is at the very bottom of Maycomb’s white society. Atticus’s sense of justice, and his defense of Tom Robinson, is a kind of assault on Ewell’s social standing. Ewell’s accusation of Tom is a fairly open manipulation of the social order; despicable as he is, he knows that his whiteness will win out in the end. In this sense Ewell seeks to exert a kind of power over the town, but in fact he is largely powerless against the likes of professional men like Atticus or Judge Taylor. So his threat against Jem and Scout can be seen as a desperate attempt to control or assert his primacy over Atticus. By harming Atticus's children, Ewell can strike back at the man who would upset Maycomb’s social order and undermine his social position, low as it is.
Once he got Tom in jail for something he did not do, he still wanted revenge on Atticus because he was able to humiliate him in front of the court. 2 down means he is trying to go after Atticus' children. These children are young and innocent but the mind of Bob Ewell is absolutely disgusting and he will do anything for revenge.
Mr Bob wanted revenge of Tom, Atticus for embarrassing him and accusing him of hitting Mayella and for revealing his living conditions. He also wanted revenge of Judge Taylor because he was the one who order Atticus for the case and he made Mr bob look like a fool when he was confessing on court.