If you have not already filed the tax returns for you and your spouse, both CRA and TurboTax recommend them you complete them "jointly" and file them together.
The reason we recommend you file this way is to ensure the correct calculations are made for any credits or benefits you may be entitled to.
Take note that although the returns are prepared together, each return will be NetFiled separately and a NetFile Confirmation Number will be issued for both you and your spouse.