Generally the taxpayer bears the burden of proof that the 90 day letter was incorrect. However, IRC §7491(a) paces the burden for proof on the commissioner if the taxpayer:
Generally those who file have made these admissions and not able to use this burden shifting law. However, non-filers can use this new law effectively in tax court. But they must continually make an offer for an out of court settlement.
Clarkson advises you to put a request for a negotiated settlement in all your correspondence and pleadings in a tax court case.