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.
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.