In normal times ... even though the payment was initiated and completed by the IRS already (meaning they have accepted the return for processing) the actual processing of balance due returns are not done until after the tax season has closed (which was 7/15/2020 this year due to the covid situation) because returns with refunds get priority. But this is not a normal year and processing is taking much longer this year due to the covid staffing shortages. Until the return has processed it may not show on the transcripts and that is OK. Unless they disagree with your filing and send you a notice in the mail you can assume everything is fine.
