Yes, if you need to file an amended tax return after IRS accepted your tax return due to a marital status change, then you will need to wait until your original tax return is processed by the IRS. If you are receiving a refund, you should wait until the check is issued. Amended returns must be filed by mail.
The article below will have the specific 2016 instructions in mid-February.
https://ttlc.intuit.com/replies/3288565
If you file your amended tax return, then you can file your joint tax return by printing and mailing it in.
Please note, it typically takes the IRS 8-12 weeks to process an amended tax return.
