I e-filed my daughter's 1099-NEC. But there's no option to pay the money due by her. How do I do that?

Was this on a separate return?

There should have been a voucher to mail with a payment. 

If not, you can print your own. 

Make sure the tax year and her social security number are noted on the memo of the check 

You filed a tax return return for her?  It didn't ask at the end how to pay the tax due?  Better check the cover instruction sheet and see how you put to pay it.  It should have printed out a 1040V voucher to mail in with a check.  

How to get a copy after filing

https://ttlc.intuit.com/community/prior-year-return/help/how-do-i-get-a-copy-of-a-return-i-filed-this-year-in-turbotax-online/00/25932

Oh and watch out if you also get 4 quarterly estimated payment slips 1040ES.  Those are not for the tax due.  They are pre payments towards next year.  You can probably ignore those unless she's getting self employment again this year.  

Thanks! We filed through eztaxreturn.com, one of the services that's authorized as free by the IRS. It sent a confirmation from the IRS that the return had been filed, but it didn't give us a copy of the return, any payment forms to print and send, or anywhere to pay the bill. And when I went to the IRS-authorized payment sites, none of them included payment options for 1099-NEC form taxes. Only various 1040 forms, which is not what she filed. 

Ok first of all this is Turbo Tax so we can't help you with other tax services.  Then she didn't file a 1099NEC .   She received a 1099NEC instead of a W2 and entered it into a 1040 tax return.  You should try to print out a copy.  So pick 2023 1040 to pay it.