@sabortooth01 you can. Look for tutorials, it will be in a folder like C:\Users\User\AppData\Roaming\Macromedia\Flash Player\#SharedObjects\3NW9VBA8, then you look for agi.armorgames.com and chat.kongregate.com for the files
Two things about the church of the chosen ones:(Spoiler alert)
ONE: You can let the guy open the church: people don't suicide until you get a graveyard in your city.
TWO: if you can make from all people 5 remaing and all the rest dead, with the church active, and don't get killed by zombies because of the low pop. them you get a ending.
Yes it should, at the end of each round. Are you not seeing it save your progress at all?