When i download my file to send to CRA, there are sections that are partially filled in and missing totals. How does turbotax fix this?

When you print to mail your return it will only be a few pages with possibly a bar code on the first page which has all the information that CRA needs from you. 

its a 12 page document

some of the totals are not filled in

TurboTax will fill in the parts that need to be completed, as per where you entered your amounts. It is possible that not every part of a form is completed- Please make sure that you clicked on Print to Mail and not just print. You need to make sure that you don't have watermarks on the pages you are sending to them.