The 990T has to be paper filed in general but can you efile the 990 and then paper file the 990T separately in ProSeries?

Yup

Do you know how? It will not allow us to efile because of the 990-T. Is there a work around for it to not try and attach the 990-T. Oddly, it allowed to efile the extension for both 990 and 990-T.

I assume that you have the box checked for "form 990 with 990T" on the information worksheet.  When you are ready to e-file the 990, click the "form 990 only " box.

THANK YOU!

You betcha!

For 2020, the IRS is REQUIRING that IRS Form 990-T be e-filed