When you say "filed an extension and have made payments every month" it sounds like you may really be referring to an installment agreement. An installment agreement is when you file a tax return and owe taxes but need more time to pay the taxes. The agreement then spreads out the payments, but your tax return was already filed.
An extension is when you need more time to actually file your tax return. For whatever reason, if you aren't able to file your return by the April deadline (April 17, 2017), then you would file a request for an extension of time to file your return. When you make this request, if you know you are going to owe some taxes but maybe aren't sure exactly how much, a lot of times people will make a payment with the extension to reduce any interest they may owe. You would place this payment in that section. If you are just making an installment agreement payments every month, you would not place that payment in that section.
When you say "filed an extension and have made payments every month" it sounds like you may really be referring to an installment agreement. An installment agreement is when you file a tax return and owe taxes but need more time to pay the taxes. The agreement then spreads out the payments, but your tax return was already filed.
An extension is when you need more time to actually file your tax return. For whatever reason, if you aren't able to file your return by the April deadline (April 17, 2017), then you would file a request for an extension of time to file your return. When you make this request, if you know you are going to owe some taxes but maybe aren't sure exactly how much, a lot of times people will make a payment with the extension to reduce any interest they may owe. You would place this payment in that section. If you are just making an installment agreement payments every month, you would not place that payment in that section.