I am in that same situation. If both T4 income and T4A income are from the same line of business it is certainly a good idea to just put all your expenses under your self-employed business. When you enter your T4A TurboTax will transfer that S-E income on a T2125. You can access that form and complete the missing information and enter your expenses.
- click Find (top right corner) --> type T4A --> click OK --> enter your T4A slip
- click Find (top right corner) --> type Self-Employment --> click OK --> complete the form and enter your expenses
