How can I file my federal and state taxes separately so I dont have to pay the additional $40 beyond the fee already associated with filing state taxes

You can file them separately with turbotax, when you get to the end of your Federal return there will be an option to either "Skip State" or Start State" you want to choose "Skip State."  However when you do go to file your state taxes you will have to pay the filing fee if you efiled your Federal, the reason for this is that with TurboTax both your Federal and State have to be filed the same way so you will not be able to efile your Federal and mail in your State.

@JillianG You most certainly eFile your Federal and paper file your state return with no Intuit charge.  But you cannot do the opposite - paper file your Federal and eFile your state.  

If you are eFileing your state you must eFile your Federal and there will be an Intuit charge.