How should I enter a 1099 for my Business's EIN when normally I have always filed my business taxes under my SSN?

In the Business info section you can enter the associated EIN for the Sch C and then in the income section you can add all the income that was received under the SS# or the EIN ... on a Sch C it doesn't make a difference. 

Weather you use the EIN or SSN doesn't amtter really. Remember, the IRS is the only issuing authority for EIN's. Therefore the IRS already knows what SSN that EIN is tied to.

You "should" be using your EIN on the SCH C anyway. You can just change it on your 2019 taxes if you want (which I recommend) and you'll be fine.