Amended return, if i have to pay back, can i set up payment plan or will the request the amount all at one time?

You can request an installment agreement from the IRS by filing form 9465. 

You will have the option to add this when you go through the File section of TurboTax. When you are asked how you want to pay your federal taxes, select Installment plan and continue through the screens to add form 9465.