No, no problem at all. And yes, in fact, you should use TurboTax self-employed. It will handle your W-2 income AND your Schedule C. You will be able to include all of your deductible business related expenses with your 1099-Misc Uber Income. Here are some links to great information that you may find helpful:
Car Sharing (Uber, Lyft) Drivers
Entering Rideshare Expenses in TurboTax
