As an accountant by training and church administrator by calling, I like church windows. It's fund accounting works nicely for keeping things seperate. Reports are not difficult and are easily understood. We have attendance of just less than 1,000 on Sundays.
Some things I don't like include: 1)Not being able to post payable invoices as they come in and just pay a few. If you have entered a bill it will be paid the next time you pay any. This means all data entry must be done just prior to printing checks. This is a inefficient. 2) Payroll module is outdated and separate from accounting. You must post payroll to the GL and corrections are extremely difficult if you use ACH. 3)Security is not granular enough.For example I cannot give the Pre-school access to just their fund in the accounting system. I have to give them access to all of A/P or G/L etc.
Overall it is not bad for the price, but it could use some work.
My level of accounting knowledge is not at all advanced. I understand the basic account types, DR/CR between account types and the difference between equity based and fund accounting. I found Church Windows to be straightforward and easy to use. I would much rather have a package that communicates between donations and accounting; maintains all the asset and fund balances natively and has all the financial reports built in.