It's up to their discretion how they handle your accounts, but if you owe less than $50,000 total then you'll be able to get another payment agreement or they'll combine your payments.
You can submit your return without paying and then apply for an installment plan (as you may have done for 2016).
Once your return has been processed, you'll receive a letter from the IRS with the tax due. At that point, they'll have a date by which you must setup a payment plan.
You should apply for the installment agreement using the same user name and password, from 2016 (if you have it), here: https://www.irs.gov/payments/online-payment-agreement-application
It's expected that you'll be required to call because you already have a payment agreement, but from inside the application you'll get special phone number, which may be faster than the general numbers they provide on their site.