I filed as married jointly and changed the return to married separately, this is when I get the warning about SSN wrong and that I should not be checking the "Spouse" box
If you are trying to use the same account that you have used in the past for a joint return, and file married filing separately, you are going to have a mess. You need to start a new account with a different user ID. As you can see.....trying to use the same account will wreak havoc with the information that transfers over from the previous year since you may be changing the order of names, etc.
Why do you want to file separate returns---usually the worst way to file?
If you were legally married at the end of 2023 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 $27,700 (+$1500 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 since with online, you get one return per fee.
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
If you are filing separately you cannot have a W-2 for your spouse in your own tax return. Her W-2 has to go in her tax return.
You should be able to use your existing TurboTax Online account if you clear your tax return and start over from scratch, without transferring any information from last year.