Since QuickBooks has all of your income (including Square), I would first enter that Form 1099-K from Square.
Then I would enter that remaining amount as cash income/receipts.
So, if QuickBooks says $100,000 income and Square has $50,000 in payments, you would enter the Form 1099-K for $50,000.
Then enter $50,000 for cash receipts so your income will still show $100,000.
