Sometimes the T5008 slips in your CRA account that are imported using Auto-Fill My Return are different from the paper copies you receive, but the totals of all amounts reported should be the same. The paper copies may have several transactions combined onto one slip, whereas the online copies have the same transactions on separate slips.
Make sure to fill in box 20 if it is missing on your slips, and your totals should be the same whether you use the imported slips or your paper slips.