I made a direct payment to the IRS for anticipated taxes based on selling ISOs. Do I enter this as a "withholding not already entered on a w2 or 1099" section?

No, withholding is not the same as an estimated tax payment.

 

 

1.  Type Estimated Tax Payments in the Search bar in the top right of your screen.  

2.  Select the Jump To Link and Choose Start next to the type of estimated tax payment you need to enter.

 

Here is a link with more details:  Estimated Tax Payments