If the 540NR is the same as the regular 540 it goes here......
To enter the amount you paid with an extension (including state extension) go to
Federal Taxes (or Personal Tab for desktop H&B version)
Deductions and Credits
Then scroll way down to Estimates and Other Taxes Paid
Other Income Taxes - Click the Start or Update button
Next page second section Payments with Extension
Either Visit All or Click Start or Update by the extension you paid