As long as you are legally married, you can file as married filing jointly or married filing separately according to your preference, which gets you a bigger refund, or even your whim, and you can switch back and forth without paperwork.
Specific to Turbotax, you can't merge accounts. You can either pick one account and add the other spouse to it, or make a new account and start fresh (this is recommended). Not because of IRS rules, but because of certain problems that can sometimes happen because of how Turbotax is programmed.
Good luck.
