TurboTax encourages you to prepare them together so it can do a better
job of optimizing, and reduce the likelihood of errors and discrepancies
between the returns. Regardless of whether you are preparing the returns together, they are always submitted individually to the CRA. You can certainly complete and submit one before the other if that's what you want, but when you've started the returns together as you have, there will be a single transaction to cover both returns.
If you want the returns to be truly separate (including paying for them separately) you'll have to start over and re-enter your information, but not choose to do a combined return this time. To do so click Tools > Return Manager and click Create a New Return. Once you have done yours, you can come back to the return manager and create another for your spouse to work on.
