By "company", do you mean you are self-employed, or you are an employee of a company based in Alberta? If you are just an employee, you just need to enter your information as usual. TurboTax will calculate if you need to pay (or be refunded) anything because of the differences in payroll taxes in the two provinces.
If you are self-employed with your company in a different province from where you live, then unfortunately you won't be able to use TurboTax, as it doesn't have the T2203 form that you would need to use.