I started to file separately this year but have since found out that it looks like were going to be paying this year. Can I go back and star over?

Yes, as long as you have not filed, you can change your filing status. 

I would suggest you use the account you used in the past year when you filed jointly and use that . 

Click on My Info just above Federal, and edit your interview. 

Yes, you can go back to the beginning and add your spouse's information to the return. Go back to the personal section and change it from married filing separately to married filing jointly and continue with the return.