The refund amount you already received should be placed line 18 for "Overpayment, if any, as shown on original return or as previously adjusted by the IRS" (if you have any trouble entering it directly, then you may need to put that on Line A under Original Return Overpayment Smart Worksheet first to get it to enter.)
So, using your numbers, your new numbers should be:
Line 11 - Your new increased total tax liability - $5,000
Line 17 - Your new total withholding and payments - $7,000
Line 18 - Your original overpayment** - $2,200
Line 19 - (Line 18-Line 17) = $4,800
Line 20 - Amount you owe (Line 11 - Line 19) = $200
**An overpayment is normally just your refund. But, sometimes people use part or all of their refund to be applied to estimated tax payments, so that is why they use the term overpayment. If you received all of your overpayment as a refund, then its just your refund. If you did apply some to ES taxes, then overpayment would be Line 75 on Form 1040 (Line 47 on Form 1040A)
