We'd like to make a partial payment to the IRS once we file and then pay the remainder in a few months. (We've already filed an extension) How can we make a partial payment once we elect to file using TurboTax?

[Opus 17]

In turbotax, select that you will pay by check.  This essentially means that you are not paying through turbotax and you can use any other method of payment (cash at 7-11, check, electronic payment, etc.) see www.irs.gov/payments  

However,

If you owe tax, you are required to pay on time even if you file an extension to submit the forms.  Therefore even if you have an extension, you are already late with your payment and accruing penalties.  You should pay as much as you can now, regardless of when you plan to submit your tax return.  see www.irs.gov/payments and make sure to select "2016 form 1040" as the reason and not a prior year or 20176 estimated payments.

The penalty for late payment is 1/2% per month of the amount due.

https://www.irs.gov/uac/newsroom/eight-facts-on-late-filing-and-late-payment-penalties

[Opus 17]

I made a correction to the penalty amount.