Last year, because the amount owed was over $1,000 dollars I ended up with four voucher payments to be used toward my 2016 taxes, I cant find where to enter these.

You'll enter any estimated payments you made in 2016 by clicking on the Federal Taxes tab, then Deductions & Credits, then scroll down to Estimates & Other Taxes Paid, and select Estimates.

You'll land on the page marked Estimated Taxes and you'll see there are sections for federal, state, and local estimates. Select the proper category and you'll be able to enter the quarterly payments you made.