I own two businesses in two different states

Each gas station has its own individual tax ID number and I received a w2 from both of them. Filed an extension for me because I didn't have all the information ready in time. I did my personal taxes with the w2 information I received from the businesses because I needed that for a loan I applied for. Only to find out that they also need the records for the businesses. 

Its been a nightmare and admittedly its my fault. My question is … Will I be ok filing for each business as an s corp even tho there is no shareholders?