I recently finished setting up a small church's QuickBooks Online accounting system, with a specific chart of accounts and with payroll. They had already started trying to get things going, but ran into trouble setting things up properly. Since churches (and other non-profit organizations) have a unique set of accounts, it is important to get assistance from a trained QuickBooks expert before you begin entering transactions into QuickBooks (either online or desktop).
Here is a link to a very helpful YouTube video which discusses using QuickBooks for a church's bookkeeping. It suggests pros and cons about QuickBooks.
I hope you find this article helpful. If you want help with QuickBooks (online or desktop versions), for your church or your small business, please do not hesitate to contact me.