Can you pay all payments from (1040V) online direct debit through one of the sites listed on IRS (ex: pay1040.com) and disregard the payment voucher?

I owe $502 total but I paid $15 to test the site
Do I need to pay $502 by check like it says on my payment voucher on turbo tax or since I paid $15 direct debit even though it doesn’t show on turbo tax account voucher  pay $487. I’m worried of not having it all in the same day.