What are you actually trying to do?
A non-profit organization can file an application to register as a 501(c)(3) organization. We can't tell you how to do that, it has nothing to do with income taxes. And generally, churches aren't required to register.
A non-profit must usually file a form 990 tax return. Churches can usually file a much simplified 990-N. We can't tell you how to do that either.
Do you want to report wages or income paid to you by a 501(c)(3)? Or do you want to take a tax deduction for donations to a non-profit?