Filing jointly is virtually always the way to file when you are married (occasionally state tax has an impact). Your situation is not a reason to file separately from your new spouse.
The tax return is equipped to handle the stimulus recovery when you have not received what you are entitled to.
A worksheet will be completed with your return. The Recovery Rebate Credit will cover both the first and second stimulus payments. This will determine the full amount of potential refund you are entitled to based on income and eligible dependents, and will be part of the final combined refund on your return, if applicable.
As far as the return where you were claimed as a dependent last year, they will reconcile their 2020 tax return using the same method to reconcile their stimulus payments.
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