Yes, if you live apart for reasons other than the end of the relationship, you must still file as married. For example, if you live apart due to work, education, or medical reasons, the Canada Revenue Agency(CRA) considers you married.
For more information, please click: TurboTax Facts Every Canadian Needs to Know About Filing Coupled Tax Returns
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Yes, You can file returns jointly. We usually recommend you prepare your returns together with your spouse because TurboTax can automatically use info from both spouses to calculate credits, benefits, etc... You can still prepare your returns separately if you want, but you'll have to manually enter some info, and perhaps even do some calculations on your own.
For more information, please review our TurboTax article: Facts Every Canadian Needs to Know About Filing Coupled Tax Returns
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