Yes, he will need to create his own account to file married filing separately. You will need to delete his income from your account and he will need to enter everything in his own account.
As xmasbaby0 mentioned, you aren't likely to pay less tax overall if you file separately. The benefit you will get from filing separately is just that you will not be held responsible to pay any tax due because of his lack of withholding.
He needs to file a new W-4 form with his employer right away and make sure that an adequate amount of tax is withheld. Click here for help with that.
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