Your return only contains your income and deductions; his return only contains his income and deductions. That's what filing separately means. The only spouse's information needed is name and social security number.
Your best option is to make two new accounts. That avoids most mistakes.
If you want to use the existing account, it "belongs" to whoever is the first-named or primary taxpayer. The person on the top line of the printed return. That spouse will change status to MFS and delete all the other spouse's income and deductions. The other spouse makes a new account and starts from scratch.
