I know you pay the 1,000 in box 4. But it was just withholding. It is just an estimate, not the actual tax. You still have to add the full 10,000 to your other income to determine the actual tax on all your income. The 10% $1,000 might not have been enough. You will get credit for the 1,000 tax withheld on 1040 line 25 b.
