"Can I use direct pay even though I choose to pay IRS with check during e-file?"
If you indicated you were going to pay your Federal taxes due with a paper check in the mail, and as long as you haven't mailed it, you can pay by any method you choose. With either method it would show up as a credit in your tax account. The IRS doesn't care "how" it gets the money as long as they receive it before the filing deadline (or postmarked before the deadline, if you end up mailing it.)
When using Direct Pay, be sure to select the correct payment type and correct tax year so it's accounted for correctly in your IRS tax account.
Indicating paying by "check" is the correct method to use when one intends to pay later by Direct Pay or the Treasury's EFTPS (for those who have an EFTPS account.)
"Can I use direct pay even though I choose to pay IRS with check during e-file?"
If you indicated you were going to pay your Federal taxes due with a paper check in the mail, and as long as you haven't mailed it, you can pay by any method you choose. With either method it would show up as a credit in your tax account. The IRS doesn't care "how" it gets the money as long as they receive it before the filing deadline (or postmarked before the deadline, if you end up mailing it.)
When using Direct Pay, be sure to select the correct payment type and correct tax year so it's accounted for correctly in your IRS tax account.
Indicating paying by "check" is the correct method to use when one intends to pay later by Direct Pay or the Treasury's EFTPS (for those who have an EFTPS account.)