It depends on which type of scenario you have:
If you are stating that you have W-2 and 1099 income for your personal tax return, then you will need to file all of your income together on your one return. TurboTax will walk you through how to enter both types of income.
OR, if you are asking from the standpoint of a business and are filing your business W-2s and 1099 forms with the government, then you will want to file them separately. W-2's and 1099s are sent to two different parts of the federal government.
To prepare your W-2s and 1099s, you can use Quick Employer Forms within TurboTax. And within Quick Employer Forms, you can e-file the federal copies of your forms to the government.
For your state filing, you will want to check your state website and see what they require as far as mailing/filing the forms together or separate.
