How are you trying to file? Your post is confusing because you started off saying this is your first time "filing MFJ", then later you are talking about filing separate returns. Which are you trying to do?
Some general information:
Filing separate returns is usually the worst way to file, especially if you have children, because you lose a lot of child-related credits. Filing separately also means both of you have to file the same way---you both have to itemize or you both have to use standard deduction. If one of you uses the itemized deductions then the other one might not have enough deductions and may not even get their standard deduction amount---thus making more of your income taxable.
If your spouse is self-employed, her business expenses go on a Schedule C. That is where she can enter expenses such as mileage, home office, supplies, etc. Itemized deductions like mortgage interest, medical expenses, property tax, etc. go on a Schedule A shared between both spouses---or divided between the two of you if you file separately.
If you file jointly, you prepare ONE tax return for both of you. All of your combined income and all of your information goes on that one return, and the refund comes with both names on it. Or the tax due is owed by the two of you.
If you file married filing separately, you have to prepare TWO returns---one for each of you. If you use online TurboTax that means using two accounts---one for each of you---and paying twice.
Your spouse is self-employed---so she must use either online Self-Employed or any version of the CD/download. You can also enter W-2 income or any other sort of income into that version. If you choose to file separately, you will need either Deluxe or Premier---or any version of the CD/download.
Using the CD/download would make the most sense for the two of you so that you could compare both ways of filing more easily.
It is not easy to compare MFJ to MFS using online TT but you can do it. Since you only get one return for each account and user ID, you have to use 3 accounts and user ID’s—one for MFJ and two for each of the MFS returns. Compare, choose, and file—and pay—accordingly.
It is much easier to do this comparison using the desktop version of TT installed from a CD or downloaded to your own computer. You pay once for the software and you can prepare multiple returns easily, and it has a “what if” feature that allows comparisons.
JOINT vs. SEPARATE RETURNS 2018 and beyond
If you were legally married at the end of 2022 your filing choices are married filing jointly or married filing separately.
Married Filing Jointly is usually better, even if one spouse had little or no income. When you file a joint return, you and your spouse will get the married filing jointly standard deduction of $25,900 (+$1400 for each spouse 65 or older) You are eligible for more credits including education credits, earned income credit, child and dependent care credit, and a larger income limit to receive the child tax credit.
If you choose to file married filing separately, both spouses have to file the same way—either you both itemize or you both use standard deduction. Your tax rate will be higher than on a joint return. Some of the special rules for filing separately include: you cannot get earned income credit, education credits, adoption credits, or deductions for student loan interest. A higher percent of your Social Security benefits may be taxable. Your limit for SALT (state and local taxes and sales tax) will be only $5000 per spouse. In many cases you will not be able to take the child and dependent care credit. The amount you can contribute to a retirement account will be affected. If you live in a community property state, you will be required to provide additional information regarding your spouse’s income. ( Community property states: AZ, CA, ID, LA, NV, NM, TX, WA, WI)
If you are using online TurboTax to prepare your returns, you will need to prepare two separate returns and pay twice.
https://ttlc.intuit.com/questions/1894449-married-filing-jointly-vs-married-filing-separately
https://ttlc.intuit.com/questions/1901162-married-filing-separately-in-community-property-states
https://ttlc.intuit.com/questions/1894449-is-it-better-for-a-married-couple-to-file-jointly-or-separ...
To begin a new joint return on TurboTax:
You will not be able to merge two previous TT account to start your new joint return. You can transfer ONE of your 2021 returns into a new return, so choose the most complicated one. The other spouse’s information needs to be entered manually.
When you enter your own information in My Info, you have to answer the question "Were you married?" If you click the button for Married, then a drop down will appear that asks, "Do you want to file this return together with your spouse?" Then you choose yes to file a joint return. You would then enter your spouse's information into My Info. Whenever you are entering income information there should then be a spot for you and for your spouse's income information. Income screens will have spots with each spouse’s name—be careful to enter under the correct names.
If you choose to file separate returns, after you say "yes" to being married, when it asks if you want to file together with your spouse, say NO. Then you will still have to enter some information about your spouse, because the IRS cross checks the SSN's to make sure you do not "double dip" and each claim the same itemized deductions.
Best Wishes!
**Disclaimer: Every effort has been made to offer the most correct information possible. The poster disclaims any legal responsibility for the accuracy of the information that is contained in this post.**
