1.Question One- I thought Balance to the force meant that the Jedi were supposed to defend but not dominate. They need both good and evil, hence the balance. I assumed The Emperor and Darth Vadar were the only Sith's alive. How is killing both of them balance? isn't it more of wiping out the Sith?
Think of the Jedi as the white blood cells in your body. How much do feel them every day? Are you even aware of what they're doing? Nope, same with the Jedi. They do not "dominate" anything, pre or post Clone Wars. Like the white blood cells, the Jedi only spring into action when something Is threatening the "balance". The Sith are a virus to the galaxy, and It's the Jedi's duty to wipe them out because their end game Is total domination.
This is why It's stated frequently in the films that the Jedi could only protect people like Amidala, but they can't fight a war for them.
2. Question 2.-In revenge of the Sith. At the plot where anakin skywalker was forced to choose to become Sith or Stay with the Jedi. The Jedi Master was close to killing the Sith Lord. Why would he kill a helpless prisoner. I thought that was against the Jedi codes?
Because for 1,000 years the Sith had waited, and plotted to destroy the Jedi, and the Republic. And now they were closer than ever to do just that. At that moment Windu realized this, and he knew that the only way to save the Galaxy was to defy the code. Sidious was literally too dangerous to be left alive.
On a side note, Sidious was no where near helpless.
3. Were their any Sith left after the series of all six movies ended. Their were thousands of Jedi in Attack of the Clones. They say a handful of Jedi escaped in "Revenge of the Sith" the only Sith I saw at the end of the series were the Emperor who died and Darth Vadar who also died. Wouldn't there be at least one more Sith somewhere who escaped?
In the movie canon no. When Vader killed the Emperor, and redeemed himself he fulfilled the Prophecy, and destroyed the last of the Sith. If there were any remaining Sith It would completely negate the entire plot of the Star Wars saga that culminated with Anakin redeeming himself, and destroying the Sith once and for all.
For the 1,000 years up to Episode 1 the Sith had followed "The Rule of Two" meaning there would ever only be 2 Sith in the Galaxy. A master, and an apprentice.