Yes, you can file your returns separately and indicate that you are common-law.
In online versions of TurboTax, you can prepare your spouse or common law partner's tax return at the same time as yours. This is called a spousal/coupled return. If you’ve already started your return but haven’t indicated that you want to prepare together, you'll need to start a new return and indicate that you want to prepare your spouse or common-law partner’s return together with yours.
TurboTax FAQ on how to file a coupled return: How do I prepare a spousal or coupled return in TurboTax Online?
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