@RebeccaTiffany 

"So what if the whole invoice was $10k no retention line and I logged a $9k payment would the p&l still show $10k received when only a partial payment was received."

Yes, in that scenario, your cash basis P&L will correctly show $9K in income.  Or, as mentioned in a previous post, the invoice can have a $9K income line and a $1K retention line (both items mapped to income accounts) and that will also show just the $9K payment received as income.  That solves the issue by allowing QB to remove A/R when running cash basis reports.  You need QB to remove the retainage receivable from your financial statements and posting it to A/R via the invoice total of $10K will do that.