How do you get in the church in assassins creed 2

If you are talking about the church in Monteriggioni that has two chests, you're going to have to invest money in it to fix it up. You can't do that, however, until you've advanced the story a bit. After doing some story missions, you'll be able to spend money on various locations around town to increase the town's value. If you spend money on the church, it'll be opened up and you can get inside.