If you have already set up an installment agreement, then you can file your return as normal through TurboTax and then instead of making a payment, you will tell the program you are going to "pay by check" and then ignore the voucher that prints out (or you can make a partial payment with it).
If you still need to set up the plan, then file the return as discussed above and then go to the link below and file for an installment agreement with the IRS.