If you are filing a joint tax return, then all of your combined income goes on the same tax return. The IRS does not care if you are living together. When you enter income on a joint return, there will be spots for each spouse on the income entry screens. Make sure you enter the income for each spouse under the correct name. If you are getting a refund, it will come in both names; if you owe tax due, it is owed by both of you.
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