What does Jem think when Atticus calls them from the balcony?

You can find the answer to this at the very start of Chapter 21. Atticus has just been made aware that his kids are up in the colored balcony and he calls them down.

When he does that, Jem comes down and is saying that "we" (in other words, his father and Tom Robinson, but he is including himself) have won the trial.  He thinks Tom will be acquitted.

This shows how naive Jem is.  He really actually thinks that there is a possibility that the jury will decide based on logic and fact.  He does not understand that the racial dynamics are going to trump everything else.