Yes, you are allowed to pay off your entire balance sooner if you wish. You would make this payment separate from your installment agreement. But, if you want to actually change the terms of the agreement - i.e. make it so that more comes out automatically every month - then you will be able to do so via your online account (accessed through the application link below) or you may have to call the IRS at 800.829.1040 after an installment agreement has been approved.
https://www.irs.gov/individuals/online-payment-agreement-application
https://www.irs.gov/payments