Hi this year I have used a CPA to file extension deadline. Now, instead of using CPA can I just file using Turbotax?

yes, the extension is for your tax return, regardless of who prepares it. 

When you requested your extension you were supposed to pay your estimated tax due.  Did you enter the payment you made into your tax return?  Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes