Profit vs loss report

@CCLDirector 

"When I run a profit and loss report it shows the deposits made into the savings accounts as part of income."

That's how it should be.  The bank account in which funds reside is not the proper indicator as to whether or not they are income.  They should be assigned to the proper equity account at the time the donation is recorded using a sales receipt or invoice.  Are you saying that all deposits made into your savings account should not be considered income?  If those donations aren't income, what are they?  If donations deposited to your savings account are not considered income, then you should go back and change the sales receipts, invoices, or deposits to properly reflect that since they were recorded as income.  If that's not feasible, you can make a journal entry to correct this by debiting income and crediting (presumably) the appropriate equity account.  If you're not comfortable with that, I strongly suggest contacting your CPA/tax accountant.