You are correct - you will file these separate tax returns in TurboTax and then you will create a new account and re-enter all of the data from both of your federal returns. That will generate a joint federal and joint California return. Once you've done that you will go on to file - tell the system you want to wait to file the federal return and just file the state return for now and then send the state returns in.
Here is a little more info for domestic partners.
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