You don't have to file your returns at the same time, but if you want to file one and hold back the other time being, you'll still need to pay for both your returns.
Not to worry, once you've paid for your returns, you can still make whatever changes you need to until you file.
It's important to note that if you've prepared your returns together, if you change something in one return it can have an impact on the calculations of the other. You'll want to make sure that if you file one, you shouldn't then make changes in the other return before you file it.
