Yes. You complete your return as married filing jointly on one account. Data transfer can only occur within the same account.
There is no way to consolidate accounts at the time. If you decide to use a new account or your account this tax year (2016) with your information for the upcoming tax year, your information entered will transfer over to next year’s tax return for 2017. You can still use one of your existing accounts moving forward, but you will not be able to transfer information from two separate accounts into one.