@RebeccaTiffany 

"Here is what our invoices look like

Foundation $10,000

Retention -$1,000

Invoice Total $9,000"

Disregard my last post.  The answer is, instead of creating the invoice as shown above, create the invoice with two line items: $9,000 Foundation and +$1,000 Retention.  When you receive the $9K payment, that will book $9K in cash basis income and you will have $1K as a receivable (accrual).  The issue with the way it's being done now is that you cannot have an asset showing on your cash basis reports without showing $10K in income.  You need that asset to go away on your cash basis balance sheet.  Doing it this way will fix it.