I have done all that.  the number will just auto-populate when you prepare or print 1099 forms.

On my company page its marked SSN.  When you preview company info before printing, it is SSN formatted.

But when you preview the 1099 it is EIN formatted.  I did a screen share with a Quickbooks person.  She saw what I was saying.  Her response was its fine.  You can go to IRS website and see that it is not fine.