To clarify, are you making these payments from QuickBooks or outside of QuickBooks and wish to only record that you've made the payments?
There's different steps you'd need to take for both ways. I'll cover both with you. (Please note: Electronic payments for taxes must be for the total amount due in order to be processed through QuickBooks payroll services. Partial "divided" payments cannot be processed).
To make the payment from QuickBooks manually:
Open the Taxes menu then choose Payroll Tax.
On the Payroll Tax Center page, you'll want to click Pay Taxes.
Select Record Payment next tot the payment you want to pay.
On the approve payment screen, you have a couple of options to choose from:
You can print a check to mail (Pay using QuickBooks) by Clicking Record and Print.
To only record the payment (When you paid outside of QuickBooks) choose Record Payment.
Also, here are a couple of articles you can check out for more details about paying taxes in QuickBooks that can come in handy: