Typically, a military filing couple will not need to file separate state returns, but if you do, below are the steps. If you post your situation and what states are involved someone may be able to assist with more specific instructions for your situation.
In online products you will need to sign up for another account besides the one used for the joint filing. In the new account you will create a "Mock" separate federal return with only your income/deductions. This will flow to a separate state return interview. You will not be filing the "Mock" separate federal return since you are filing jointly at the federal level, so you will need to print/mail the separate state return.
You can use the same process in a desktop (CD/Download) product. The advantage in the desktop is you can create/file the joint returns and create the separate returns all in the same product.
Here is a link with more details if needed.
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