You have two options, you can pay as much as you can through direct debit from your bank and e-file your tax return.
The other option is to select to pay the taxes owed with a check and e-file your tax return. Then never send a check.
You can also use the IRS payment website to pay any taxes owed. If you do use this option then for your tax return use the option to pay by check and never send a check since you have made payment on the IRS website - https://www.irs.gov/payments
