I am a nurse. I currently work at a school and a hospital. Last year I had W-2s. This year I will add a 1099 contracted position to my work life. How will this effect me?

I file quarterly for the independent contractor work, and annually for my W-2 positions? Does TurboTax handle complicated taxes like this? I'm thinking of using Quickbooks for invoices and expenses. Thank you for your help!