I have paid what I owe to Federal tax due for my 1099-misc via 1040ES. Do I put the amount I paid in estimated tax within the 1099-MISC "Federal tax with-held" box?
No. You'll enter 1040-ES payments in the Estimates & Other Taxes Paid section under the Deductions & Credits tab when you get to that point in the program. Enter your 1099-MISC exactly as printed, and press on.