You need to enter the W-2s exactly as reported.  You can then enter the child care expenses you paid.  

If you have only one child, only 3,000 of expenses would be eligible for the credit, but since more than $3,000 was paid from your FSA, there would be no credit.  $1,000 of your FSA would become taxable.

Up to $6,000 of expenses would be eligible if you have more than one child.  Since you overcontributed, $1,000 of your withheld amount will become taxable income, so up to $1,000 of your expense could be used to create a credit.