Balance due returns are low man on the totem pole and will most likely not be processed until 7/15 or later. The online payment option on the IRS site should allow you to make a payment on the 2019 form 1040. If you cannot figure this out then you can mail in a payment instead ... send a 1040-V with the payment :
Who at the IRS told you they had not received your filing? If you are relying on the IRS refund tracking web site, you can't use that to track a tax return where there is no refund.
When you say transmitted, did you efile your return and was it accepted, or did you print and mail your return yourself?
You can verify an efiled return was submitted and accepted using this link: https://shop.turbotax.intuit.com/efile/efile_status_lookup.jsp
If you printed and mailed your return, the IRS did not process any mailed returns for several weeks so it's not likely they would know whether they received it or not unless they have opened it and started processing it.