How should Jews and Christians be treated?
With kindness and patience.
2:109
Many of the people of the Scripture long to make you disbelievers.... Forgive and be indulgent (toward them) until Allah give command.
By Fighting against them.
9:29
Fight against such of those who have been given the Scripture as believe not in Allah.
The Quran was revealed based on events for 23 years. The verse 2:109 is talking about the treatment of the Jews and Christians in general, where verse 9:29 is talking about a situation where the rulers of the Jewish and Christian states are preventing the people from having the free well to choose their religion and worship God as they believe is correct.